Variant report

Variant	rs593239
Chromosome Location	chr11:57667111-57667112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57666728..57668740-chr11:57669401..57671347,2	MCF-7	breast:
2	chr11:57666968..57668868-chr11:57669771..57671757,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10750870	0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs10792110	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10792118	0.85[EUR][1000 genomes]
rs10896644	1.00[ASW][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10896649	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10896653	0.84[ASN][1000 genomes]
rs11229109	0.89[JPT][hapmap];0.81[YRI][hapmap]
rs11229170	0.85[EUR][1000 genomes]
rs11229171	0.85[EUR][1000 genomes]
rs11229172	0.85[EUR][1000 genomes]
rs11229173	0.83[EUR][1000 genomes]
rs11229183	0.83[EUR][1000 genomes]
rs11570176	1.00[ASW][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs11570181	1.00[ASW][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs12270209	0.82[ASN][1000 genomes]
rs12363024	0.81[ASN][1000 genomes]
rs12366063	0.83[EUR][1000 genomes]
rs12420220	0.83[EUR][1000 genomes]
rs12805343	0.81[ASN][1000 genomes]
rs1424753	0.81[ASN][1000 genomes]
rs1624389	0.81[ASN][1000 genomes]
rs17455422	1.00[ASW][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs17455626	0.81[ASN][1000 genomes]
rs1783818	0.82[ASN][1000 genomes]
rs1783824	0.81[ASN][1000 genomes]
rs1783976	0.81[ASN][1000 genomes]
rs1783978	0.81[ASN][1000 genomes]
rs1783979	1.00[ASW][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs1783980	0.81[ASN][1000 genomes]
rs1783981	0.81[ASN][1000 genomes]
rs1785498	0.81[ASN][1000 genomes]
rs1785499	0.81[ASN][1000 genomes]
rs1786438	0.83[ASN][1000 genomes]
rs2156638	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2956981	0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs2956982	0.81[ASN][1000 genomes]
rs3017889	0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs36036499	1.00[ASW][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs4245215	0.84[EUR][1000 genomes]
rs4611222	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs471398	0.83[ASN][1000 genomes]
rs547118	0.83[ASN][1000 genomes]
rs56392705	0.81[ASN][1000 genomes]
rs585337	0.83[ASN][1000 genomes]
rs585761	0.84[ASN][1000 genomes]
rs588612	0.86[ASN][1000 genomes]
rs588713	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs588808	0.84[ASN][1000 genomes]
rs591322	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs592785	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600488	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs602861	0.89[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs606499	0.83[ASN][1000 genomes]
rs606731	0.86[EUR][1000 genomes]
rs615133	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs616911	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs623541	0.83[ASN][1000 genomes]
rs626043	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs627145	0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs633129	0.85[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs636388	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs639158	0.83[ASN][1000 genomes]
rs644219	0.84[ASN][1000 genomes]
rs645145	0.84[ASN][1000 genomes]
rs652191	0.89[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs652908	0.83[ASN][1000 genomes]
rs653889	1.00[ASW][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs658936	0.83[ASN][1000 genomes]
rs6591443	0.83[EUR][1000 genomes]
rs659165	0.84[ASN][1000 genomes]
rs662638	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs665058	0.88[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs666021	0.86[JPT][hapmap]
rs671508	0.84[ASN][1000 genomes]
rs681397	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs682258	0.84[ASN][1000 genomes]
rs686489	0.86[ASN][1000 genomes]
rs7105506	0.81[ASN][1000 genomes]
rs7115528	0.87[ASN][1000 genomes]
rs7117020	0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs7119973	0.83[EUR][1000 genomes]
rs7120868	1.00[ASW][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs7479922	0.81[ASN][1000 genomes]
rs7943793	0.85[EUR][1000 genomes]
rs7948571	0.84[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs593239	TIMM10	cis	parietal	SCAN
rs593239	UBE2L6	cis	parietal	SCAN
rs593239	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs593239	TIMM10	cis	cerebellum	SCAN
rs593239	YPEL4	cis	lung	GTEx
rs593239	OR4C6	cis	parietal	SCAN

Chromatin state (count:20 , 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	chr11:57666400-57667400	Enhancers	Stomach Mucosa	stomach
9	chr11:57666400-57668400	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr11:57666400-57669200	Enhancers	Fetal Intestine Large	intestine
11	chr11:57666400-57671200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:57666400-57671200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:57666400-57672000	Enhancers	HMEC	breast
14	chr11:57666600-57667200	Enhancers	Small Intestine	intestine
15	chr11:57666600-57667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:57666800-57667600	Enhancers	Colonic Mucosa	Colon
17	chr11:57666800-57667600	Enhancers	Duodenum Mucosa	Duodenum
18	chr11:57666800-57667800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:57666800-57672000	Enhancers	Fetal Intestine Small	intestine
20	chr11:57667000-57667200	Enhancers	Esophagus	oesophagus

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