Variant report

Variant	rs4949875
Chromosome Location	chr1:76173080-76173081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76171538..76176296-chr1:76182594..76187669,7	K562	blood:
2	chr1:76171242..76173918-chr1:76251777..76253452,2	MCF-7	breast:
3	chr1:76171640..76173855-chr1:76188377..76192246,4	K562	blood:
4	chr1:76171478..76174682-chr1:76188816..76193676,7	K562	blood:

Variant related genes	Relation type
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1061337	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10873685	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11161437	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161468	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11161493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs11161510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11161511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs11161515	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11161521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11163924	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1146579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1146580	0.86[EUR][1000 genomes]
rs1146581	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1146588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs12091720	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094842	0.86[EUR][1000 genomes]
rs12123977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs12126481	0.85[EUR][1000 genomes]
rs12126607	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs12127402	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12134854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12136754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1250874	0.86[EUR][1000 genomes]
rs1251075	0.85[EUR][1000 genomes]
rs1251078	0.96[CEU][hapmap]
rs1251079	0.96[CEU][hapmap]
rs1303169	0.84[EUR][1000 genomes]
rs1313071	0.85[EUR][1000 genomes]
rs1498312	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498316	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611823	0.85[EUR][1000 genomes]
rs1612097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1694419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1694424	0.81[EUR][1000 genomes]
rs17587071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1767455	0.81[EUR][1000 genomes]
rs1767456	0.86[EUR][1000 genomes]
rs1767458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1770511	0.85[EUR][1000 genomes]
rs1855136	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1858536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1890451	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1890452	0.87[EUR][1000 genomes]
rs2066183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211717	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211718	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211737	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2153126	0.87[EUR][1000 genomes]
rs2173378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2185152	0.89[EUR][1000 genomes]
rs2185435	0.87[EUR][1000 genomes]
rs2185436	0.87[EUR][1000 genomes]
rs2211080	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2275378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs2788654	0.86[EUR][1000 genomes]
rs28602663	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs380075	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs392691	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4559448	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4646961	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4949674	0.92[EUR][1000 genomes]
rs4949872	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949877	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4949879	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56267813	0.82[EUR][1000 genomes]
rs56352044	0.82[EUR][1000 genomes]
rs57186386	0.87[EUR][1000 genomes]
rs60378926	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61289992	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61622554	0.90[EUR][1000 genomes]
rs61797339	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61797340	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61799967	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61799988	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61799990	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6593514	0.87[EUR][1000 genomes]
rs6593515	0.85[EUR][1000 genomes]
rs6593585	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6688749	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72686191	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7513363	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7513559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515955	0.81[EUR][1000 genomes]
rs7516122	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7516226	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7518038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7524467	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7533888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539246	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7541058	0.84[EUR][1000 genomes]
rs7544117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546641	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7548962	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7549167	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7550974	0.87[EUR][1000 genomes]
rs7552404	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554984	0.83[EUR][1000 genomes]
rs8763	1.00[CHB][hapmap]
rs942270	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662166	0.89[AMR][1000 genomes];0.89[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	nsv871572	chr1:76161889-76208488	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4949875	MSH4	cis	Artery Tibial	GTEx
rs4949875	ACADM	cis	Muscle Skeletal	GTEx
rs4949875	ACADM	cis	Whole Blood	GTEx
rs4949875	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76172400-76173600	Enhancers	Hela-S3	cervix
2	chr1:76172800-76173400	Enhancers	K562	blood

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