Table 3 Novel and reported SNPs for association analysis
Gene | Gen location | Allele | Amino acid (AA) | Change of AA class | AA position | SNP IDa |
|---|---|---|---|---|---|---|
RXRA | Exon 1 | [C/T] | Pro (P) | Ser (S) | 8 | rs209839910 |
Intron 1 | [A/G] | ------ | ------ | ------ | g.105,985,004 | |
Intron 1 | [G/T] | ------ | ------ | ------ | g.105,985,027 | |
Intron 1 | [T/G] | ------ | ------ | ------ | g.105,985,044 | |
Intron 1 | [G/A] | ------ | ------ | ------ | g.105,985,130 | |
Intron 1 | [C/T] | ------ | ------ | ------ | g.105,986,006 | |
Exon 2 | [A/G] | Ser (S) | No change | 136 | g.105,986,149 | |
Exon 3 | [G/T] | Val (V) | No change | 148 | g.105,986,715 | |
Exon 3 | [A/C] | Asn (N) | Thr (T) | 162 | rs137184653 | |
Exon 4 | [C/T] | Pro (P) | Leu (L) | 198 | g.105,989,022 | |
Exon 4 | [C/T] | Thr (T) | No change | 217 | g.105,989,080 | |
Intron 4 | [G/A] | ------ | ------ | ------ | g.105,989,114 | |
Intron 4 | [A/G] | ------ | ------ | ------ | g.105,989,179 | |
Intron 4 | [T/C] | ------ | ------ | ------ | g.105,989,219 | |
Intron 4 | [T/C] | ------ | ------ | ------ | g.105,989,236 | |
Intron 4 | [G/A] | ------ | ------ | ------ | g.105,989,283 | |
Exon 5 | [G/A] | Arg (R) | Lys (L) | 245 | g.105,989,790 | |
Intron 5 | [G/A] | ------ | ------ | ------ | g.105,989,983 | |
Intron 5 | [A/C] | ------ | ------ | ------ | g.105,990,023 | |
Exon 7 | [G/A] | Pro (P) | No change | 357 | g. 105,990,568 | |
Exon 8 | [T/C] | Arg (R) | No change | 370 | rs136289117 | |
Intron 9 | [G/A] | ------ | ------ | ------ | g.106,004,142 | |
Intron 9 | [A/C] | ------ | ------ | ------ | g.106,004,147 | |
Intron 9 | [G/A] | ------ | ------ | ------ | g.106,004,180 | |
Intron 9 | [A/G] | ------ | ------ | ------ | g.106,004,184 | |
Intron 10 | [T/C] | ------ | ------ | ------ | g.106,004,449 | |
Intron 10 | [C/A] | ------ | ------ | ------ | g.106,004,518 | |
Intron 12 | [G/A] | ------ | ------ | ------ | g.106,009,252 | |
Intron 12 | [G/A] | ------ | ------ | ------ | g.106,009,293 | |
Intron 12 | [C/T] | ------ | ------ | ------ | g.106,011,088 | |
Intron 12 | [C/G] | ------ | ------ | ------ | g.106,011,096 | |
Intron 12 | [T/G] | ------ | ------ | ------ | g.106,011,126 | |
Exon 13 | [C/T] | Ile (I) | No change | 667 | g.106,011,238 | |
Exon 13 | [C/T] | Pro (P) | No change | 672 | g.106,011,253 | |
Intron 13 | [C/T] | ------ | ------ | ------ | g.106,011,448 | |
Intron 13 | [C/T] | ------ | ------ | ------ | g.106,011,466 | |
Intron 13 | [G/A] | ------ | ------ | ------ | g.106,011,539 | |
IGF1R | Exon 1 | [T/C] | Ser (S) | No change | 4 | rs379619394 |
Exon 1 | [A/G] | Gly (G) | Arg (R) | 6 | rs385718425 | |
Exon 1 | [C/A] | Leu (L) | Ile (I) | 25 | rs209595810 | |
Exon 1 | [T/G] | Ile (I) | Met (M) | 28 | rs380419725 | |
Exon 1 | [T/G] | Ser (S) | Ile (I) | 29 | rs378266791 | |
Exon 2 | [T/C] | Cys (C) | No change | 33 | rs134868883 | |
Exon 7 | [T/C] | Asp (D) | No change | 491 | rs41961336 | |
Exon 7 | [A/C] | Thr (T) | Pro (P) | 496 | rs135514117 | |
Exon 7 | [C/T] | Ser (S) | Pro (P) | 497 | rs132825686 | |
Exon 8 | [C/T] | Ala (A) | No change | 583 | rs385548776 | |
Exon 10 | [C/T] | Asp (D) | No change | 675 | rs210778604 | |
Exon 11 | [C/T] | Thr (T) | No change | 773 | rs209736678 | |
Exon 12 | [G/A] | Pro (P) | No change | 837 | rs41640706 | |
Exon 13 | [C/T] | Ser (S) | No change | 881 | rs133373507 | |
Exon 16 | [C/T] | Tyr (Y) | No change | 987 | rs208140993 | |
Exon 19 | [G/A] | Lys (K) | No change | 1168 | rs380900001 | |
Exon 21 | [G/A] | Ser (S) | No change | 1308 | rs384753755 | |
TCF15 | Exon 1 | [C/G] | Asp (D) | Glu (E) | 32 | rs134079367 |
Exon 1 | [T/G] | Ser (S) | Ala (A) | 37 | rs137532487 | |
Exon 1 | [A/C] | Gln (Q) | Pro (P) | 73 | rs134702498 | |
Intron 1 | [G/A] | ------ | ------ | ------ | g.60,997,442 | |
INS | Exon 1 | [G/A] | Ala (A) | Thr (T) | 24 | rs383254521 |
Intron 1 | G/A | ------ | ------ | ------ | g.50,036,892 | |
Intron 1 | C/T | ------ | ------ | ------ | g.50,036,987 | |
Intron 1 | A/G | ------ | ------ | ------ | g.50,037,033 | |
Exon 2 | [T/G] | Val (V) | Gly (G) | 63 | rs135743222 | |
Exon 2 | [C/T] | Pro (P) | Leu (L) | 72 | rs109490717 | |
Exon 2 | [C/T] | Pro (P) | Leu (L) | 80 | rs109229312 | |
EGFR | Exon 1 | [T/C] | Lys (K) | Arg (R) | 29 | rs136877925 |
Exon 4 | [T/C] | Asn (N) | Asp (D) | 182 | rs135955902 | |
Exon 6 | [T/G] | His (H) | Pro (P) | 233 | rs137416447 | |
Exon 7 | [A/G] | Asn (N) | No change | 280 | rs209095847 | |
Exon 8 | [C/T] | Val (V) | Ile (I) | 318 | rs211658253 | |
Exon 18 | [T/C] | Ser (S) | No change | 720 | rs210170316 | |
Exon 21 | [T/C] | Ala (A) | No change | 839 | rs110045273 | |
Exon 25 | [G/A] | Arg (R) | No change | 999 | rs379217506 | |
Exon 28 | [G/A] | Val (V) | No change | 1107 | rs385131275 | |
USF1 | Intron 2 | A/G | ------ | ------ | ------ | g.8,458,558 |
Intron 3 | G/A | ------ | ------ | ------ | g.8,458,837 | |
Intron 6 | A/G | ------ | ------ | ------ | g.8,459,971 | |
Exon 8 | C/T | Ser (S) | No change | 236 | g.8,460,354 | |
Intron 9 | C/T | ------ | ------ | ------ | g.8,460,878 |