Variant report

Variant	rs7548962
Chromosome Location	chr1:76139266-76139267
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	chr1:76138876..76140835-chr1:76251753..76254513,3	K562	blood:
2	chr1:76138718..76140997-chr1:76142345..76144918,2	K562	blood:

Variant related genes	Relation type
ENSG00000137955	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000207241	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

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

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv2756846	chr1:76083408-76156986	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7548962	MSH4	cis	Artery Tibial	GTEx
rs7548962	ACADM	cis	Whole Blood	GTEx
rs7548962	MSH4	cis	Esophagus Muscularis	GTEx
rs7548962	ACADM	cis	Muscle Skeletal	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76137600-76139400	Flanking Active TSS	K562	blood
2	chr1:76137800-76139400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:76137800-76139400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:76137800-76139400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:76137800-76139400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:76137800-76139800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:76138000-76139400	Enhancers	HMEC	breast
8	chr1:76138000-76139600	Enhancers	Placenta	Placenta
9	chr1:76138200-76139400	Enhancers	Lung	lung
10	chr1:76138600-76139400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:76138800-76139400	Enhancers	HepG2	liver
12	chr1:76138800-76142200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:76138800-76143000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:76139000-76142400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:76139000-76142600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:76139000-76142600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:76139000-76142600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:76139000-76142800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:76139000-76143000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:76139000-76143400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:76139200-76143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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