Variant report

Variant	rs1498312
Chromosome Location	chr1:76177849-76177850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76177430..76180048-chr1:76194109..76196652,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1061337	0.93[EUR][1000 genomes]
rs10873685	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11161437	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161468	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11161493	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11161510	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs11161511	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11161515	0.94[EUR][1000 genomes]
rs11161521	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs11163924	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146574	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1146579	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1146580	0.91[EUR][1000 genomes]
rs1146581	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1146588	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12091720	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094842	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12123977	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12126481	0.90[EUR][1000 genomes]
rs12126607	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12127402	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12136754	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs1250874	0.91[EUR][1000 genomes]
rs1251075	0.90[EUR][1000 genomes]
rs1303169	0.88[EUR][1000 genomes]
rs1313071	0.90[EUR][1000 genomes]
rs1498315	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498316	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611823	0.90[EUR][1000 genomes]
rs1612097	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1694419	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1694424	0.86[EUR][1000 genomes]
rs17587071	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1767455	0.86[EUR][1000 genomes]
rs1767456	0.91[EUR][1000 genomes]
rs1767458	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1770511	0.90[EUR][1000 genomes]
rs1855136	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1858536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1890451	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1890452	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2066183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211717	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211718	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211737	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2153126	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2173378	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs2185152	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2185435	0.91[EUR][1000 genomes]
rs2185436	0.91[EUR][1000 genomes]
rs2211080	0.86[EUR][1000 genomes]
rs2275378	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2788654	0.91[EUR][1000 genomes]
rs28602663	0.90[EUR][1000 genomes]
rs380075	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818855	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs392691	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4559448	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4646961	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4949674	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4949872	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949874	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949875	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949876	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]
rs4949877	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4949879	0.89[EUR][1000 genomes]
rs56267813	0.82[EUR][1000 genomes]
rs56352044	0.82[EUR][1000 genomes]
rs57186386	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60378926	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61289992	0.93[EUR][1000 genomes]
rs61622554	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61797339	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61797340	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs61799967	0.94[EUR][1000 genomes]
rs61799988	0.85[EUR][1000 genomes]
rs61799990	0.87[EUR][1000 genomes]
rs6593514	0.91[EUR][1000 genomes]
rs6593515	0.90[EUR][1000 genomes]
rs6593585	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6688749	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72686191	0.94[EUR][1000 genomes]
rs7513363	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7513559	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]
rs7515955	0.81[EUR][1000 genomes]
rs7516122	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7516226	0.90[EUR][1000 genomes]
rs7518038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7524467	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7533888	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539246	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7541058	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7544117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546641	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7548962	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7549167	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7550974	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7552404	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554984	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8763	1.00[CHB][hapmap]
rs942270	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662166	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
rs1498312	ACADM	cis	Whole Blood	GTEx
rs1498312	ACADM	cis	Muscle Skeletal	GTEx
rs1498312	MSH4	cis	Artery Tibial	GTEx
rs1498312	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76176400-76178200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:76177000-76178600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:76177400-76178800	Enhancers	Stomach Smooth Muscle	stomach
4	chr1:76177600-76179000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:76177800-76178000	Enhancers	Adipose Nuclei	Adipose
6	chr1:76177800-76178600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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