TABLE 3.
Transmission of type 1 diabetes–associated SNP alleles in total and stratified sets of T1DGC families
| Chromosome | SNP | Gene | Method for affected sib-pair family stratification |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| None (n = 4,663) | HLA IBD (n = 1,558) | HLA Non-IBD (n = 2,026) | DR3 (n = 635) | DR4 (n = 1,088) | DR34 (n = 1,246) | DRxx (n = 283) | INS_AA (n = 1,647) | INS_Tx (n = 641) | Female (n = 968) | Male (n = 1,108) | Young (n = 429) | Old (n = 269) | |||
| 1p13 |
rs2476601 |
PTPN22 |
50.3 |
4.4 |
12.1 |
— |
4.2 |
3.5 |
— |
7.4 |
2.3 |
2.7 |
3.5 |
3.2 |
— |
| 2q24 |
rs3747517 |
IFIH1 |
5.3 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 2q33 |
rs231727 |
CTLA4 |
11.7 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 6p21 |
rs2187668 |
DQA1 |
202.1 |
84.7 |
8.6 |
70.9 |
44.2 |
88.2 |
— |
37.1 |
11.8 |
19.2 |
39.5 |
14 |
5.1 |
| 6p21 |
rs7454108 |
DRB1 |
230.9 |
124.1 |
58.3 |
17.5 |
104.4 |
97 |
2.2 |
83.5 |
31.3 |
51.5 |
50.3 |
19.7 |
7.8 |
| 6q25 |
rs1738074 |
TAGAP |
3.3 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 10p15 |
rs12722495 |
IL2RA |
10.6 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 10p15 |
rs947474 |
PRKCQ |
3.2 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 10q23 |
rs10509540 |
RNLS |
14.1 |
— |
— |
— |
— |
— |
— |
3.3 |
— |
— |
— |
— |
— |
| 11p15 |
rs689 |
INS |
77.2 |
6.5 |
15.3 |
— |
4 |
7.3 |
4 |
NA |
NA |
5.1 |
5.2 |
— |
— |
| 12p13 |
rs4763879 |
CD69 |
3.8 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 12q13 |
rs2292239 |
IKZF4 |
9.9 |
— |
2.3 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 12q24 |
rs3184504 |
SH2B3 |
14.5 |
— |
— |
— |
2.5 |
— |
— |
— |
— |
— |
— |
— |
— |
| 15q25 |
rs3825932 |
CTSH |
3.9 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 16p13 |
rs12708716 |
CLEC16A |
8.9 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 17q12 |
rs2290400 |
GSDML |
4.9 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 18p11 |
rs478582 |
PTPN2 |
3.9 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 18q22 |
rs763361 |
CD226 |
5.4 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 19q13 |
rs425105 |
PRKD2 |
3.7 |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
— |
| 20p13 | rs2281808 | SIRPG | 5.6 | — | — | — | — | — | — | — | — | — | — | — | — |
ASPs were previously genotyped at 53 SNPs as part of the T1DGC GWAS (6). Transmission of alleles was analyzed in these families by TDT. Results are shown as the negative log(P). Only SNPs that had −logP values >3 in the total family collection were studied further. Families were stratified according to criteria described in the text and TDT scores calculated for the 20 SNPs shown. In this case, scores were corrected for multiple testing by subtracting 2.38, the log of the number of tests (n = 240); only values >2.2 are shown. “Gene” does not necessarily indicate the causal gene but the gene either containing or very near the most disease-associated SNP or a gene of strong functional candidacy in the associated region.