Variant report

Variant	rs7544117
Chromosome Location	chr1:76158246-76158247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76157193..76160004-chr1:76260955..76264534,3	K562	blood:
2	chr1:76158085..76160004-chr1:76262153..76264534,2	K562	blood:
3	chr1:76156186..76158840-chr1:76189632..76191650,2	K562	blood:
4	chr1:76157340..76160559-chr1:76189001..76191132,3	K562	blood:

Variant related genes	Relation type
ENSG00000178193	Chromatin interaction
ENSG00000057468	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1061337	0.85[EUR][1000 genomes]
rs10873685	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11161437	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161468	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11161493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11161510	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs11161511	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11161515	0.86[EUR][1000 genomes]
rs11161521	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs11163924	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1146579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1146580	0.94[EUR][1000 genomes]
rs1146581	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1146588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs12091720	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12094842	0.82[EUR][1000 genomes]
rs12123977	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12126481	0.82[EUR][1000 genomes]
rs12126607	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12127402	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12134854	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1250874	0.94[EUR][1000 genomes]
rs1251075	0.94[EUR][1000 genomes]
rs1251077	0.80[AFR][1000 genomes]
rs1251078	0.96[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs1251079	0.96[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs1303169	0.92[EUR][1000 genomes]
rs1313071	0.93[EUR][1000 genomes]
rs1498312	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498316	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498317	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1611823	0.94[EUR][1000 genomes]
rs1612097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1613437	0.84[EUR][1000 genomes]
rs1694419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1694424	0.89[EUR][1000 genomes]
rs17587071	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs1767455	0.89[EUR][1000 genomes]
rs1767456	0.94[EUR][1000 genomes]
rs1767458	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1770511	0.93[EUR][1000 genomes]
rs1855136	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890451	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1890452	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2066183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211717	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211718	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211737	1.00[ASN][1000 genomes]
rs2153126	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2173378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs2185152	0.86[EUR][1000 genomes]
rs2185435	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2185436	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2275378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2788654	0.94[EUR][1000 genomes]
rs28602663	0.82[EUR][1000 genomes]
rs380075	0.95[ASN][1000 genomes]
rs3818855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs392691	1.00[ASN][1000 genomes]
rs4559448	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4646961	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949674	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949872	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949877	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949879	0.81[EUR][1000 genomes]
rs57186386	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60378926	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61289992	0.85[EUR][1000 genomes]
rs61622554	0.87[EUR][1000 genomes]
rs61797339	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61797340	0.86[EUR][1000 genomes]
rs61799967	0.86[EUR][1000 genomes]
rs61799969	0.82[EUR][1000 genomes]
rs6593514	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6593515	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6593585	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688749	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72686191	0.85[EUR][1000 genomes]
rs7513363	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515955	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7516122	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516226	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7518038	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524467	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7533888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534754	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7535991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539246	0.88[EUR][1000 genomes]
rs7541058	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7546641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548962	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549167	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550974	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7552404	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554984	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8763	1.00[CHB][hapmap]
rs942270	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9662166	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv945914	chr1:76109781-76172388	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7544117	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76157400-76158400	Weak transcription	K562	blood

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