Table 6.
Bioinformatic characterization of SNPs in linkage disequilibrium with rs8111699 in European Population (HaploReg V4).
| Locus | ReferenceSNPs | LD (r2) EUR | Chromatin states a | H3K4me1 b | H3K4me3 c | H3K27a d | H3K9ac e | Dnase | |
|---|---|---|---|---|---|---|---|---|---|
| Adult liver (AL) | HepG2 (H) | ||||||||
| 5 kb 5' of STK11 | rs7253626 | 0.9 | – | – | – | – | – | – | |
| 1.6kb 5' of STK11 | rs7254997 | 0.97 | EnhW2 | EnhAF | AL, H | AL | AL, H | AL, H | – |
| intronic | rs7256801 | 1 | TxReg | TxReg | AL | AL, H | AL, H | AL, H | H |
| intronic | rs12611000 | 0.95 | TxEnh5 | TxEnh5 | AL, H | AL, H | AL, H | AL, H | – |
| intronic | rs8111699 | 1 | TxEnh5 | TxReg | AL, H | H | AL, H | AL, H | H |
| intronic | rs7259033 | 0.92 | TxReg | TxEnh5 | AL, H | AL, H | AL | AL, H | H |
| intronic | rs8106285 | 0.87 | – | – | AL | – | AL | AL | – |
| intronic | rs34928889 | 0.81 | – | – | – | – | AL | – | – |
| intronic | rs11084889 | 0.94 | – | – | – | – | AL | – | – |
| intronic | rs60977562 | 0.96 | – | – | AL | – | AL | – | – |
| intronic | rs60490879 | 0.96 | – | – | – | – | – | – | – |
| intronic | rs7253853 | 0.95 | – | – | – | – | – | – | – |
| 3'-UTR | rs10415095 | 0.92 | – | – | – | – | – | – | – |
EUR, European population; LD, linkage disequilibrium.
a
Chromatin states based on 25-state model: EnhW2, Weak Enhancer 2; EnhAF, Active Enhancer Flank; TxReg, Transcribed & regulatory (promoter/enhancer); TxEnh5, Transcribed 5' preferential and Enhancer.
b
H3K4me1 is a histone mark associated with enhancers and DNA regions downstream of transcription starts.
c
H3K4me3 is a histone mark associated with promoters that are active or poised to be active.
d
H3K27ac is a histone mark that indicates active enhancers, promoters or active transcription sites.
e
H3K9ac is a histone mark connected with active promoters.