Variant report

Variant	rs592785
Chromosome Location	chr11:57666611-57666612
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10750870	0.85[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10792110	0.85[CEU][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10896644	0.81[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10896649	0.85[CEU][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10896653	0.83[ASN][1000 genomes]
rs11229109	0.89[JPT][hapmap]
rs11570176	0.81[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs11570181	0.81[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs12270209	0.81[ASN][1000 genomes]
rs1424752	0.84[LWK][hapmap]
rs17455422	0.81[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1783818	0.81[ASN][1000 genomes]
rs1783979	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs1786438	0.84[ASN][1000 genomes]
rs2156638	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs2956981	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs3017889	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs36036499	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs4611222	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs471398	0.84[ASN][1000 genomes]
rs480933	0.81[LWK][hapmap]
rs483030	0.84[LWK][hapmap]
rs501054	0.81[LWK][hapmap]
rs527140	0.84[LWK][hapmap]
rs530094	0.84[LWK][hapmap]
rs541245	0.82[LWK][hapmap]
rs544446	0.84[LWK][hapmap]
rs547118	0.84[ASN][1000 genomes]
rs585337	0.84[ASN][1000 genomes]
rs585761	0.83[ASN][1000 genomes]
rs588612	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs588713	0.86[ASN][1000 genomes]
rs588808	0.83[ASN][1000 genomes]
rs591322	0.84[ASN][1000 genomes]
rs593239	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600488	0.84[ASN][1000 genomes]
rs602861	0.81[CEU][hapmap];0.95[GIH][hapmap]
rs606499	0.84[ASN][1000 genomes]
rs612688	0.84[LWK][hapmap]
rs615133	0.82[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.83[ASN][1000 genomes]
rs616911	0.82[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.84[ASN][1000 genomes]
rs623541	0.84[ASN][1000 genomes]
rs626043	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627145	0.85[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs633129	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs636388	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs639158	0.84[ASN][1000 genomes]
rs644219	0.83[ASN][1000 genomes]
rs645145	0.83[ASN][1000 genomes]
rs652191	0.81[CEU][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs652908	0.84[ASN][1000 genomes]
rs653889	0.81[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs658936	0.84[ASN][1000 genomes]
rs659165	0.83[ASN][1000 genomes]
rs665058	0.85[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs666021	0.86[JPT][hapmap]
rs671508	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs681397	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs682258	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs686489	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7115528	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7117020	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs7120868	0.80[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs7948571	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs592785	YPEL4	cis	lung	GTEx
rs592785	TIMM10	cis	multi-tissue	Pritchard
rs592785	OR4C6	cis	parietal	SCAN
rs592785	TIMM10	cis	parietal	SCAN
rs592785	YPEL4	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57660600-57671200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:57664600-57672000	Weak transcription	Right Atrium	heart
3	chr11:57666000-57667800	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr11:57666200-57668400	Enhancers	K562	blood
5	chr11:57666200-57670800	Enhancers	NHEK	skin
6	chr11:57666200-57673000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr11:57666200-57673200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:57666400-57666800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:57666400-57667000	Enhancers	HSMMtube	muscle
10	chr11:57666400-57667400	Enhancers	Stomach Mucosa	stomach
11	chr11:57666400-57668400	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr11:57666400-57669200	Enhancers	Fetal Intestine Large	intestine
13	chr11:57666400-57671200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:57666400-57671200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:57666400-57672000	Enhancers	HMEC	breast
16	chr11:57666600-57667200	Enhancers	Small Intestine	intestine
17	chr11:57666600-57667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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