Variant report

Variant	rs7946258
Chromosome Location	chr11:62255694-62255695
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62252877..62255736-chr11:62313013..62315240,2	MCF-7	breast:
2	chr11:62254167..62256598-chr11:62317883..62320645,2	MCF-7	breast:
3	chr11:62255238..62256844-chr11:62323475..62325357,2	MCF-7	breast:
4	chr11:62255336..62257193-chr11:62370913..62372418,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257058	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000149499	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10897285	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231108	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231110	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231111	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231112	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11231115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231117	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231119	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231120	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11231121	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11231130	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11819950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822224	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11826756	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827029	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223424	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12271287	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273682	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12281588	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12281651	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12289932	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12291022	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294680	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157332	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157338	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157363	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17157365	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35117866	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3867144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4124	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234858	0.91[ASN][1000 genomes]
rs56973213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57973105	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295893	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105793	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7123692	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7124044	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7124130	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7127582	0.93[AMR][1000 genomes]
rs73500219	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951639	1.00[CEU][hapmap];1.00[JPT][hapmap]

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	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription 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	1401 gene(s)	inside rSNPs	diseases
5	nsv345	chr11:62225251-62270254	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv897621	chr11:62230309-62290170	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62231200-62264600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:62247800-62257000	Weak transcription	NHLF	lung
3	chr11:62247800-62264600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr11:62247800-62266600	Weak transcription	Esophagus	oesophagus
5	chr11:62247800-62272600	Weak transcription	Aorta	Aorta
6	chr11:62248600-62256800	Weak transcription	NH-A	brain
7	chr11:62248600-62264600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:62248800-62258800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:62249000-62256800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:62249000-62256800	Weak transcription	A549	lung
11	chr11:62249000-62264600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:62252000-62256200	Enhancers	Placenta	Placenta
13	chr11:62252200-62257000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:62254000-62257400	Enhancers	Fetal Stomach	stomach
15	chr11:62254200-62256200	Enhancers	HepG2	liver
16	chr11:62254400-62255800	Enhancers	Fetal Intestine Small	intestine
17	chr11:62254400-62256400	Enhancers	Fetal Lung	lung
18	chr11:62255000-62255800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:62255000-62255800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:62255000-62256200	Enhancers	Fetal Intestine Large	intestine
21	chr11:62255200-62255800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr11:62255200-62255800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:62255200-62255800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr11:62255200-62256400	Enhancers	Fetal Muscle Leg	muscle
25	chr11:62255200-62258000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:62255400-62255800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:62255400-62255800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
28	chr11:62255400-62255800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:62255400-62255800	Enhancers	Brain Substantia Nigra	brain
30	chr11:62255400-62255800	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr11:62255400-62256200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr11:62255400-62256200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr11:62255400-62257200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:62255400-62257600	Enhancers	Adipose Nuclei	Adipose
35	chr11:62255400-62258600	Weak transcription	K562	blood
36	chr11:62255600-62255800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:62255600-62255800	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr11:62255600-62255800	Flanking Active TSS	Rectal Smooth Muscle	rectum
39	chr11:62255600-62255800	Enhancers	Osteobl	bone
40	chr11:62255600-62257000	Enhancers	Stomach Smooth Muscle	stomach
41	chr11:62255600-62257400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:62255600-62258000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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