Variant report

Variant	rs12669619
Chromosome Location	chr7:87514832-87514833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:87504491-87515461	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:87504848..87507366-chr7:87513350..87516160,4	MCF-7	breast:
2	chr7:87511127..87515461-chr7:87518832..87520793,3	MCF-7	breast:

Variant related genes	Relation type
DBF4	TF binding region
ENSG00000075303	Chromatin interaction
ENSG00000006634	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1015415	1.00[CEU][hapmap]
rs10215700	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10215973	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10226830	0.82[EUR][1000 genomes]
rs10226849	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10227951	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10230718	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10232457	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10237097	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10237201	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10238564	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10239908	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10239922	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10244734	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10245767	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10246786	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];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247258	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10252990	1.00[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10253106	1.00[ASW][hapmap];0.86[CEU][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10259182	0.91[EUR][1000 genomes]
rs10260007	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10264856	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10268868	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10269158	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10276499	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10276819	1.00[CEU][hapmap];0.90[CHB][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];0.94[ASN][1000 genomes]
rs10952899	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12532279	0.91[EUR][1000 genomes]
rs12532941	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12533477	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12539395	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12540032	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13438651	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17149864	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs17150009	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073985	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2106522	0.87[EUR][1000 genomes]
rs2157926	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2188527	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2188828	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2214101	0.87[EUR][1000 genomes]
rs2214106	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285646	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2285649	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2373574	0.89[EUR][1000 genomes]
rs28437979	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28449219	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28449354	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28537604	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28546778	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28627774	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28642834	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28645115	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28774398	0.91[EUR][1000 genomes]
rs28831998	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58638862	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59058733	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465117	0.87[EUR][1000 genomes]
rs6465118	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6948061	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6952943	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6972098	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73706914	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73706916	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73706922	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73706924	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73706950	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790722	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7798074	1.00[CEU][hapmap];0.90[CHB][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];0.94[ASN][1000 genomes]
rs7801337	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9655954	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9655955	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs976602	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs992422	0.91[EUR][1000 genomes];0.89[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	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:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87506600-87516800	Weak transcription	Left Ventricle	heart
2	chr7:87506600-87518800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:87506600-87534400	Weak transcription	Gastric	stomach
4	chr7:87506600-87535200	Weak transcription	Esophagus	oesophagus
5	chr7:87506600-87536800	Weak transcription	Lung	lung
6	chr7:87506600-87539600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:87506600-87539600	Weak transcription	Pancreas	Pancrea
8	chr7:87506800-87540400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:87507000-87536400	Weak transcription	Placenta	Placenta
10	chr7:87507200-87519400	Weak transcription	Fetal Stomach	stomach
11	chr7:87507200-87527000	Weak transcription	Liver	Liver
12	chr7:87507200-87528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:87507200-87531800	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:87507200-87532400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:87507200-87534000	Weak transcription	Brain Angular Gyrus	brain
16	chr7:87507200-87537000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:87507200-87538400	Weak transcription	Adipose Nuclei	Adipose
18	chr7:87507200-87539200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:87507600-87520400	Weak transcription	Colonic Mucosa	Colon
20	chr7:87507600-87539400	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:87507800-87519800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:87507800-87521600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:87507800-87532400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:87507800-87532400	Weak transcription	Brain Germinal Matrix	brain
25	chr7:87508000-87515000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:87508000-87516800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr7:87508000-87516800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:87508000-87516800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:87508000-87517000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr7:87508000-87518600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:87508000-87523000	Weak transcription	Brain Anterior Caudate	brain
32	chr7:87508000-87526600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:87508000-87530000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:87508000-87535400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr7:87508000-87535800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:87508000-87537400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:87508000-87538200	Weak transcription	Thymus	Thymus
38	chr7:87508200-87516800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:87508200-87516800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:87508200-87520000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr7:87508200-87521800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:87508200-87524600	Weak transcription	NHLF	lung
43	chr7:87508200-87530400	Weak transcription	Fetal Brain Male	brain
44	chr7:87508200-87537400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:87508200-87538400	Weak transcription	Fetal Brain Female	brain
46	chr7:87508200-87538600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr7:87508200-87539000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:87508200-87539200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr7:87508200-87539400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:87508200-87539600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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