Table 2 SCC susceptibility novel loci that replicated at P < 0.05 in 23andMe cohort
rsID | Locus | CHR | BP | EA | NEA | EAF | log (OR) | SE | P | Nearest gene | eQTL gene (skin) | eQTL gene P value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
rs3768321 | 3 | 1 | 40,035,928 | T | G | 0.19 | 0.041 | 0.007 | 1.32E-09 | PABPC4 (0) | PABPC4 | 2.65E-28 |
rs12142181 | 4 | 1 | 41,912,985 | T | C | 0.08 | −0.054 | 0.010 | 2.41E-08 | EDN2 (−31.46 kb) | EDN2 | 6.26E-05 |
rs17391694 | 6 | 1 | 78,623,626 | T | C | 0.10 | 0.054 | 0.008 | 2.12E-12 | GIPC2 ( + 20.51 kb) | FUBP1 | 5.49E-15 |
rs3851290 | 13 | 1 | 205,149,508 | T | C | 0.39 | −0.039 | 0.006 | 1.17E-12 | DSTYK (0) | DSTYK | 5.52E-18 |
rs1260326 | 14 | 2 | 27,730,940 | C | T | 0.41 | −0.030 | 0.005 | 3.57E-08 | GCKR (0) | NRBP1 | 3.09E-18 |
rs9878566 | 18 | 3 | 156,493,213 | T | C | 0.48 | 0.034 | 0.005 | 3.52E-10 | LINC00886 (0) | LINC00886 | 1.56E-24 |
rs6889986 | 24 | 5 | 90,207,399 | A | G | 0.44 | −0.041 | 0.005 | 6.75E-14 | GPR98 (0) | – | 8.94E-11 |
rs77758638 | 33 | 8 | 42,014,917 | T | C | 0.11 | 0.045 | 0.008 | 4.35E-08 | AP3M2 (0) | POLB/AP3M2 | 4.39E-26 |
rs35563099 | 40 | 10 | 119,572,403 | T | C | 0.15 | −0.046 | 0.007 | 1.19E-10 | RAB11FIP2 (−192kb) | – | |
rs2924552 | 42 | 11 | 68,889,367 | T | C | 0.41 | 0.049 | 0.005 | 3.19E-19 | TPCN2 ( + 31.3 kb) | TPCN2 | 2.18E-05 |
rs10899466 | 44 | 11 | 78,013,674 | A | G | 0.18 | −0.061 | 0.007 | 1.47E-16 | GAB2 (0) | GAB2 | 1.24E-13 |
rs10876864 | 47 | 12 | 56,401,085 | A | G | 0.41 | 0.031 | 0.005 | 5.95E-09 | SUOX ( + 1.78 kb) |IKZF4 (−13 kb) | SUOX/IKZF4 | 3.97E-54/ 9.86E-9 |
rs142004400 | 53 | 14 | 50,829,560 | C | A | 0.03 | −0.109 | 0.014 | 4.83E-14 | CDKL1 (0) | CDKL1 (eQTL Gen) | 1.13E-19 |
rs10141120 | 55 | 14 | 103,923,008 | C | T | 0.35 | −0.047 | 0.006 | 5.18E-17 | MARK3 (0) | MARK3/CKB | 7.60E-39/ 3.33E-31 |
rs472385 | 57 | 15 | 44,186,844 | A | G | 0.25 | −0.035 | 0.006 | 1.37E-08 | FRMD5 (0) | AC011330.5 | 5.74E-19 |
