Variant report

Variant	rs7644325
Chromosome Location	chr3:52081136-52081137
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	chr3:52063546..52065859-chr3:52080631..52082453,2	MCF-7	breast:
2	chr3:52077892..52079847-chr3:52080984..52082911,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12495536	0.81[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12496447	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12629791	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13316105	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2334961	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28387060	0.80[EUR][1000 genomes]
rs2878438	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34162321	0.89[ASN][1000 genomes]
rs352152	0.93[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4687607	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687805	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687810	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6773704	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6777340	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6778442	0.93[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6786592	0.85[EUR][1000 genomes]
rs72964039	0.85[AFR][1000 genomes]
rs731684	1.00[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs735768	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs747343	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs749995	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7616695	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642787	0.87[ASN][1000 genomes]
rs7642881	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs893055	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs9828327	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9848727	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9851576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866081	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9874939	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1792042	chr3:52070955-52091254	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1793040	chr3:52070955-52091254	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv1797975	chr3:52070955-52091254	Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv1798814	chr3:52070955-52091254	Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
15	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52074000-52083200	Weak transcription	Pancreas	Pancrea
2	chr3:52074400-52083200	Weak transcription	Liver	Liver
3	chr3:52076000-52081400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52076000-52081600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:52076000-52086400	Weak transcription	Fetal Brain Male	brain
6	chr3:52076600-52081600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:52077200-52081800	Enhancers	Brain Substantia Nigra	brain
8	chr3:52077400-52081600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr3:52077400-52081800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:52077400-52082400	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:52077400-52082400	Enhancers	Esophagus	oesophagus
12	chr3:52077600-52081800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:52077600-52083400	Enhancers	Brain Angular Gyrus	brain
14	chr3:52077800-52082400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:52077800-52082400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr3:52077800-52083400	Weak transcription	Primary B cells from cord blood	blood
17	chr3:52078000-52081800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:52078000-52083200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52078000-52083400	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:52078000-52084000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:52078200-52083800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:52078200-52084200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:52078400-52081600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:52078400-52081800	Enhancers	Right Ventricle	heart
25	chr3:52078400-52082200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:52078600-52081400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:52078600-52084200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:52078800-52081600	Enhancers	Placenta	Placenta
29	chr3:52078800-52083200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:52078800-52083200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:52079000-52081400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:52079200-52081200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:52079200-52081600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:52079200-52081800	Enhancers	Lung	lung
35	chr3:52079200-52082000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:52079200-52082000	Weak transcription	Primary T cells from cord blood	blood
37	chr3:52079200-52082200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr3:52079200-52082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:52079200-52082400	Enhancers	Fetal Muscle Leg	muscle
40	chr3:52079400-52081400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:52079400-52081400	Weak transcription	Thymus	Thymus
42	chr3:52079400-52081600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:52079400-52082000	Enhancers	Left Ventricle	heart
44	chr3:52079400-52082200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:52079400-52082200	Enhancers	Right Atrium	heart
46	chr3:52079400-52082400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
47	chr3:52079400-52082400	Enhancers	Spleen	Spleen
48	chr3:52079400-52082600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:52079400-52082800	Enhancers	HUVEC	blood vessel
50	chr3:52079600-52081200	Flanking Active TSS	NHEK	skin

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