Variant report

Variant	rs7938563
Chromosome Location	chr11:67304131-67304132
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	chr11:67303244..67305352-chr11:67315972..67317504,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11601325	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs11605586	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1695	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1871034	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1871036	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871042	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs2370141	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs34721562	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34802338	0.97[EUR][1000 genomes]
rs4084113	0.86[JPT][hapmap]
rs4320958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465371	0.86[JPT][hapmap]
rs4891	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4930430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4930431	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs57808037	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs611663	0.83[CEU][hapmap]
rs6591244	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591245	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6591251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6591252	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6591256	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs7106423	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7106675	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs7114510	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs749174	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs762803	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs7934075	0.81[EUR][1000 genomes]
rs7941395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs7941648	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs7948478	0.80[EUR][1000 genomes]
rs7948823	0.82[EUR][1000 genomes]
rs7952081	0.96[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs917570	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs947895	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
4	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer 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	176 gene(s)	inside rSNPs	diseases
5	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
6	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
7	nsv521723	chr11:67175692-67311258	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
8	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
9	nsv1052919	chr11:67252337-67306030	Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv541078	chr11:67252337-67306030	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7938563	ATG2A	cis	parietal	SCAN
rs7938563	GSTP1	cis	parietal	SCAN
rs7938563	PTPRCAP	cis	Heart Left Ventricle	GTEx
rs7938563	RPS6KB2	cis	Lymphoblastoid	GTEx
rs7938563	RPS6KB2	cis	multi-tissue	Pritchard
rs7938563	PTPRCAP	cis	Nerve Tibial	GTEx
rs7938563	RTN3	cis	parietal	SCAN
rs7938563	NDUFV1	cis	parietal	SCAN
rs7938563	RPS6KB2	cis	lymphoblastoid	seeQTL
rs7938563	TBC1D10C	cis	parietal	SCAN
rs7938563	GSTP1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67301400-67310800	Weak transcription	Pancreas	Pancrea
2	chr11:67303400-67304600	Enhancers	Fetal Intestine Small	intestine
3	chr11:67303600-67304600	Enhancers	Fetal Intestine Large	intestine

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