23andMe: SNPs So Nice They Call Them Twice

...with all of the duplicates tabulated below.

If you've tested with 23andMe and you've gotten the Complete Edition, you can download your raw data. What you'll get is a file containing the results for each SNP that was tested.

For each SNP, there's a line in the file containing:

• the id number of the SNP (starting with "rs" for a standard SNP id, or with "i" for one of 23andMe's internal identifiers);
• the chromosome the SNP is on;
• the location of the SNP on that chromosome;
• your genotype for that SNP.

Nearly 600,000 SNPs are tested for, so this file is fairly large.

Now, if you look closely at the data, you'll find that some of the locations are there twice. The two instances have different id numbers, but the same chromosome and the same location. Sometimes the two genotypes they'll give for you are the same, and sometimes they're different.

In fact, there are two locations that are reported three times, under three different names.

I've compiled a list of all the duplicate 23andMe SNPs, as of April 26, 2010, along with the possible alleles (variants) reported for each one.

So, why does 23andMe include these apparent duplicates? The duplicate SNPs fall into two distinct categories, and the rationale may be different for these two different types.

 

Category 1: The duplicate SNPs all have the same possible alleles.

For example, on chromosome 2, location 38151881 is reported both as i3002894 and as rs28936413, and both of them are C/T SNPs (that is, C and T are the only values tested for, and reported, on that SNP).

For the Category 1 duplicates, some are simply SNPs that have been given two different rs labels in the literature. But most of them involve 23andMe's internal identifiers (starting with i instead of rs). Perhaps some of these are there as quality control — testing the same SNP in two different ways on the chip. It's conceivable (although it seems unlikely to me) that some of these have different flanking base sequences on the chip, in which case they would be testing for different things.

 

Category 2: The duplicate SNPs have different possible alleles.

For example, on chromosome 1, location 156921704 is reported both as i3002777 (an A/T SNP) and as i3002778 (a G/T SNP).

The Category 2 SNPs are more interesting than the Category 1 SNPs, as we'll see.

First, though, we need to take a brief detour...

In general, DNA consists of a sequences of bases, each one an A, C, G, or T. (It's actually a sequence of base pairs, but only one base is reported in each pair, since the other base is complementary and is determined by the first one.)

The vast majority of DNA, more than 99.9% of the base pairs, is the same in all human beings. But with more than 3 billion base pairs in the human genome, even a 0.1% difference between two individuals comes to more than 3 million differences.

These differences take a variety of forms. For example, there can be entire base sequences that are present in some people but absent in others (insertions and deletions). Segments can be repeated a varying number of times (copy number variation). Segments can be reversed in some individuals. But the simplest kind of variation is where a substantial segment of DNA is the same in everybody except that the base in one specific location in the segment varies: maybe some people have an A at that location, and some people have a C.

These are called SNPs — single-nucleotide polymorphisms — specific locations in our DNA where there are differences between people, but where the surrounding bases are the same for everybody (or nearly everybody).

Theoretically the four bases A, C, G, and T can occur at any SNP. However, most of these SNPs are biallelic. This means that, at that location, only two alleles actually appear there if you look throughout the population. So we might describe a SNP as an A/C SNP, for example, if everybody (or nearly everybody) has either an A or a C for that SNP.

But a very small number of locations are triallelic — if you look in a number of people, you'll find three different bases appearing at that spot, not just two. Even more rarely, you'll find SNPs where all four bases appear in the population.

The Illumina chip can apparently test directly for some of these triallelic SNPs. For example, rs3091244 (location 157951289 on Chromosome 1) is an A/G/T SNP. The genotype reported for rs3091244 any particular individual will be a pair of bases where each base is an A, G, or T.

Now, it looks like there are additional triallelic, or potentially triallelic, SNPs that 23andMe has decided to handle by testing for the possible alleles in pairs. For instance, look at location 156921704 on chromosome 1. 23andMe has defined one SNP i3002777 to test for A vs. T, and a second SNP i3002778 to test for G vs. T.

I don't know if these Category 2 SNPs are known to be triallelic, or if 23andMe is just unsure as to which bases may appear at each one. It's also possible that 23andMe wants to double-check some normal biallelic SNPs to be sure that they're not getting spurious results, or to see if they really are biallelic.

 
THE TABLES

Category 1
Biallelic Locations Appearing Under More than One SNP ID at 23andMe
The Category 1 SNPs below all have just two alleles being tested for, but under more than one SNP id. Four of these locations are slightly different from the others; these four are highlighted in yellow:

• On Chromosome 1, location 153472258 has three SNP ids, not just two.
• On Chromosome 9, location 131616165 is a D/I (base deleted/inserted) SNP.
• On Chromosome 22, location 40854188 is also a D/I (base deleted/inserted) SNP.
• Also on Chromosome 22, location 40855030 is a D/I (base deleted/inserted) SNP.

Chromosome (or MT for the mitochondrial DNA) and Location		First SNP Name	Second SNP Name	Third SNP Name, if any	Alleles Tested For
1	153472258	i4000415	i4000416	i4000385	C / T
2	38151881	i3002894	rs28936413		C / T
2	138476119	rs1801105	i3000469		C / T
2	240595439	rs1138444	rs13848		C / T
4	100575360	rs1154470	i4001505		A / G
6	31429660	rs1058067	rs11547339		C / T
6	32913027	rs2239701	i4001510		C / T
6	80967459	i4000422	i4000423		A / G
7	99108158	i3003582	rs41279857		G / T
9	131616165	i4000446	i4000447		D / I
11	6372010	i4000430	i4000431		G / T
11	116212197	i3002724	rs28931575		A / G
11	116212979	i3002723	rs28931574		C / G
11	116213026	i3002692	rs28929476		A / C
12	101761584	i3003403	rs5030856		C / T
12	101770784	i3003400	rs5030850		A / G
12	101770811	i3003399	rs5030847		A / G
12	101784540	i3003397	rs5030843		C / T
15	70429913	i4000436	i4000395		C / T
15	70429973	i4000441	i4000440		A / G
19	46550761	rs1800470	rs1982073		A / G
22	40852557	rs1135840	i4001403		C / G
22	40852565	rs28371736	i4001398		A / G
22	40852582	rs28371735	i4001394		A / G
22	40852909	rs28371732	i4001438		C / T
22	40853749	rs28371725	i4001476		C / T
22	40853787	i3003610	i4001471		C / G
22	40853802	i4001466	rs5030867		G / T
22	40853977	rs28371723	i4001426		A / T
22	40854188	i4000452	i4001497		D / I
22	40854254	rs28371717	i4001478		A / C
22	40854434	rs28371715	i4001440		A / G
22	40854640	rs2267447	i4001392		C / T
22	40854761	i4001480	rs5030866		C / T
22	40854979	rs5030865	i4001433		A / C
22	40854988	rs1135824	i4001452		C / T
22	40855021	rs28371710	i4001421		C / T
22	40855030	rs5030655	i4001420		D / I
22	40855700	rs1081003	i4001386		A / G
22	40855716	rs28371706	i4001501		A / G
22	40856614	rs5030862	i4001414		C / T
22	40857477	rs28624811	i4001444		A / G
22	40858326	rs1080985	i4001488		C / G
Y	13378470	i3000047	rs2032601		C / T
Y	14085184	i3000052	rs2032661		A / G
Y	14096856	i3000051	rs2032656		G / T
Y	17080420	i3000075	rs3897		A / G
Y	20071555	i4000245	i4000137		A / G
Y	20330026	i3000077	rs2032625		A / G
Y	20332274	i3000072	rs2032622		A / T
Y	20338197	i3000079	rs2032628		A / T
Y	20353795	i3000082	rs2032637		A / G
MT	228	rs41323649	i3001447		A / G
MT	295	rs41528348	i4001145		C / T
MT	458	rs41356551	i3001450		C / T
MT	464	rs41402146	i3001451		C / T
MT	712	i3001941	rs28358568		C / T
MT	771	rs2853519	i3001949		A / G
MT	829	rs28358569	i3001954		A / G
MT	3395	rs41460449	i3001456		C / T
MT	3548	rs28358586	i3002611		A / G
MT	3721	rs41355750	i3001457		A / G
MT	3844	rs28357971	i3002117		A / G
MT	3916	rs41524046	i3001458		A / G
MT	3993	rs41402945	i3001460		C / T
MT	4025	i1000001	i3001461		A / G
MT	4337	rs41456348	i3001462		C / T
MT	4562	i1000011	i3001463		C / T
MT	4825	rs28357978	i3001467		A / G
MT	4918	rs28357980	i3002607		A / G
MT	5005	rs41419549	i3001469		C / T
MT	5047	rs28357983	i3001470		A / G
MT	5264	i1000006	i3001471		C / T
MT	5391	rs41333444	i3001473		A / G
MT	5443	rs3020601	i3003119		C / T
MT	5461	rs3021088	i3001474		A / G
MT	5657	i1000002	i3001475		A / G
MT	5774	rs35855595	i3002264		A / G
MT	6027	i1000008	i3001476		A / G
MT	6046	i1000007	i3001477		C / T
MT	6153	i1000013	i3001479		C / T
MT	6222	rs28358869	i3001480		C / T
MT	6366	rs41464546	i3000564		C / T
MT	6681	i1000014	i3001482		C / T
MT	6753	i1000003	i3001485		A / G
MT	6777	i1000015	i3001487		C / T
MT	7056	rs1978002	i3000601		A / G
MT	7176	rs28358874	i3002612		C / T
MT	7197	rs28358875	i3000604		A / C
MT	7522	i1000010	i3001488		A / G
MT	7769	rs41534044	i3000652		A / G
MT	8278	i1000016	i3001490		C / T
MT	8415	rs28358884	i3000721		C / T
MT	8469	rs1116907	i3000730		C / T
MT	8617	rs41427749	i3001491		G / T
MT	8656	rs2853822	i3002650		C / T
MT	8830	rs2000976	i3000775		C / T
MT	8870	i1000004	i3001493		A / G
MT	9094	rs41513156	i3001495		A / G
MT	9450	rs28358272	i3000835		C / T
MT	9541	rs2248727	i3001497		C / T
MT	9555	i3000848	rs28358273		A / G
MT	9699	rs9743	i3003523		C / T
MT	9717	rs41502750	i3001498		C / T
MT	9900	rs41345446	i3001499		C / T
MT	10035	rs41347846	i3001500		C / T
MT	10311	rs41467651	i3001502		A / G
MT	10374	rs28358277	i3000915		A / G
MT	10587	rs28358281	i3002609		A / G
MT	10811	rs28358282	i3000954		C / T
MT	10820	rs28358283	i3000956		A / G
MT	11378	rs41537746	i3001505		A / G
MT	11900	rs28718242	i3001506		C / T
MT	11948	rs28359168	i3001065		A / G
MT	11970	rs28359169	i3001507		A / G
MT	12190	rs28505538	i3001088		C / T
MT	12415	rs41520546	i3001509		C / T
MT	12631	rs41445245	i3001510		A / G
MT	12670	rs41369547	i3001511		C / T
MT	13781	rs41358152	i3001513		A / G
MT	13966	rs41509754	i3001515		C / T
MT	14179	rs28357671	i3001517		C / T
MT	14213	rs28357672	i3002604		C / T
MT	14567	rs28357677	i3001304		A / G
MT	14583	rs41354845	i3001518		A / G
MT	14770	i3001320	rs28357679		A / G
MT	14784	rs28357680	i3001520		C / T
MT	15245	rs28357369	i3001521		A / G
MT	15258	rs41518645	i3001522		A / G
MT	15302	rs28573847	i3001523		A / G
MT	15759	rs41337244	i3001525		A / G
MT	15785	rs28357375	i3002602		C / T
MT	15834	rs41504845	i3001526		C / T
MT	15905	rs35788393	i3001527		C / T
MT	15908	rs41383248	i3001528		A / G
MT	15929	rs28357377	i3001529		A / G
MT	15931	rs41441949	i3001530		A / G
MT	15943	rs28535186	i3001436		C / T
MT	16164	rs41479950	i4000851		A / G
MT	16272	rs2857290	i3001782		C / T
MT	16329	rs41355449	i3001851		C / T
MT	16392	rs41378955	i3001902		A / G
MT	16393	rs34301918	i3001539		A / G

 

Category 2
Triallelic Locations Appearing Under More than One SNP ID at 23andMe
The Category 2 SNPs below all have at least three alleles being tested for (they may be triallelic). Two are slightly different from the others; again, these are highlighted in yellow:

• On the Y chromosome, location 20224669 has one SNP id where three alleles are tested for, and a second SNP id where two of those same alleles are tested for again.
• On the mitochondrial DNA, location 16148 has all four alleles being tested for.

Chromosome (or MT for the mitochondrial DNA) and Location		1st SNP Name and Alleles Tested For		2nd SNP Name and Alleles Tested For		3rd SNP Name, if any, and Alleles Tested For
1	156921704	i3002777	A/T	i3002778	G/T
3	10158808	i3003387	C/G	i3003388	A/C
3	10166488	i3003389	C/G	i3003390	C/T
Y	20224669	i4000064	A/G/T	i4000065	A/T
MT	317	i4001006	C/T	i4001007	A/C
MT	3197	rs28434229	A/G	i3002050	C/G
MT	3286	rs28537613	A/T	i3002059	C/T
MT	3497	i4001370	G/T	i4000820	A/G
MT	3797	rs28357970	A/T	i3002114	A/G
MT	4455	rs28439204	A/T	i3002168	C/T
MT	4905	i4000986	A/C	i4001044	C/T
MT	5332	i4000655	A/C	i4000656	C/T
MT	8451	rs28461343	G/T	i3000729	C/T
MT	9823	i4000687	A/C	i4000688	C/T
MT	10734	rs28709356	A/C	i3000947	C/T
MT	10886	i4000576	C/T	i4000575	A/T
MT	12634	rs3926883	A/C	i3001129	C/T
MT	13959	i4000552	C/G	i4000562	A/G
MT	14561	rs28357676	A/G	i3001302	C/G
MT	15044	rs28357684	A/G	i3001344	C/G
MT	15851	i4001345	C/T	i4001346	G/T
MT	15885	rs28617642	A/G	i3001429	C/G
MT	16148	i4000638	C/T	i4000639	C/G	i4000727	A/C
MT	16158	i4001383	C/T	i4000643	A/T
MT	16167	i4000843	A/C	i4000844	A/G
MT	16170	i4000787	C/T	i4000788	A/C
MT	16177	i4001354	A/C	i4001356	C/T
MT	16208	i4001124	A/G	i4001123	A/C
MT	16209	i4001117	A/T	i4001126	A/G
MT	16216	i4001057	C/T	i4001058	A/C
MT	16220	i4000794	C/T	i4000795	A/C
MT	16230	i4000859	C/T	i4000861	C/G
MT	16234	i4000855	C/T	i4000858	A/C
MT	16308	i4001210	C/T	i4001209	C/G
MT	16526	i4000692	A/C	i4000693	A/G