Variant report

Variant	rs12538627
Chromosome Location	chr7:87495725-87495726
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	chr7:87493589..87495813-chr7:87498469..87500039,2	MCF-7	breast:
2	chr7:87495680..87498675-chr7:87503191..87505606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006634	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1015415	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10215700	0.98[ASN][1000 genomes]
rs10215973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10216040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10230718	0.98[ASN][1000 genomes]
rs10231033	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10231094	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10232449	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10235854	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239922	0.98[ASN][1000 genomes]
rs10244734	0.98[ASN][1000 genomes]
rs10245617	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10245767	1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10247258	0.93[ASN][1000 genomes]
rs10248345	0.91[ASN][1000 genomes]
rs10249603	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252226	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10253864	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254392	1.00[CEU][hapmap]
rs10255051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258021	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10259182	0.93[ASN][1000 genomes]
rs10261685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10263074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264991	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10266417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268868	0.98[ASN][1000 genomes]
rs10269158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10275831	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10276409	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10278483	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs10280397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280686	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10280904	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10281645	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10486997	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10487000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972683	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11982729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532279	0.93[ASN][1000 genomes]
rs12532358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533477	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12535013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12537294	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12540931	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13437761	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13438341	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17149840	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17149864	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[ASN][1000 genomes]
rs17149924	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17149946	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17149963	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17150006	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17150008	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169578	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041049	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2106522	0.86[ASN][1000 genomes]
rs2188523	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2188530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2214101	0.86[ASN][1000 genomes]
rs2373574	0.93[ASN][1000 genomes]
rs28375568	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379741	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28470575	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28535601	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28535947	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537604	0.98[ASN][1000 genomes]
rs28546778	0.98[ASN][1000 genomes]
rs28572147	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28624877	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28627774	0.98[ASN][1000 genomes]
rs28666506	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28742881	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28774398	0.93[ASN][1000 genomes]
rs28879532	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28890472	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148727	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4148729	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6465117	0.86[ASN][1000 genomes]
rs6465118	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs6948061	0.98[ASN][1000 genomes]
rs6952943	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6955897	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6957599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7794263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9655953	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9655954	0.98[ASN][1000 genomes]
rs976602	0.93[ASN][1000 genomes]
rs9986978	0.80[AMR][1000 genomes];0.86[EUR][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	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1023352	chr7:87418818-88192925	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv539005	chr7:87418818-88192925	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87460600-87498000	Weak transcription	Fetal Heart	heart
2	chr7:87470200-87499600	Weak transcription	NHEK	skin
3	chr7:87471200-87499800	Weak transcription	NHLF	lung
4	chr7:87473200-87495800	Weak transcription	Lung	lung
5	chr7:87475000-87495800	Weak transcription	Aorta	Aorta
6	chr7:87475000-87495800	Weak transcription	Spleen	Spleen
7	chr7:87475000-87500000	Weak transcription	Gastric	stomach
8	chr7:87481000-87503800	Weak transcription	NH-A	brain
9	chr7:87481200-87504000	Weak transcription	Osteobl	bone
10	chr7:87482200-87503200	Weak transcription	HMEC	breast
11	chr7:87486000-87504400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:87486400-87504800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:87486800-87499600	Weak transcription	HSMM	muscle
14	chr7:87487000-87501800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:87487400-87503800	Weak transcription	HUVEC	blood vessel
16	chr7:87487600-87497000	Weak transcription	Fetal Kidney	kidney
17	chr7:87487600-87497000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:87487800-87499800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:87488000-87499800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:87488000-87499800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:87488000-87500200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:87488000-87503400	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:87488200-87495800	Weak transcription	Brain Substantia Nigra	brain
24	chr7:87488200-87500000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:87488200-87504600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr7:87488400-87499800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr7:87488400-87500000	Weak transcription	Hela-S3	cervix
28	chr7:87489000-87495800	Weak transcription	Liver	Liver
29	chr7:87489000-87499600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr7:87489600-87499800	Weak transcription	HepG2	liver
31	chr7:87489600-87500200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:87489600-87500400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:87491400-87503600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:87492000-87501000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr7:87493000-87502600	ZNF genes & repeats	GM12878-XiMat	blood
36	chr7:87493800-87496400	ZNF genes & repeats	Brain Germinal Matrix	brain
37	chr7:87493800-87497800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:87494000-87496600	Strong transcription	A549	lung
39	chr7:87494000-87497000	ZNF genes & repeats	Fetal Intestine Large	intestine
40	chr7:87494000-87497200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:87494200-87496000	ZNF genes & repeats	Ovary	ovary
42	chr7:87494200-87497600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
43	chr7:87494200-87498800	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr7:87494400-87498200	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr7:87494400-87498800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr7:87494600-87500800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
47	chr7:87494800-87495800	Strong transcription	Left Ventricle	heart
48	chr7:87494800-87496000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
49	chr7:87494800-87496200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:87494800-87496400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

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