Variant report

Variant	rs4712924
Chromosome Location	chr6:25389208-25389209
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25387854..25389408-chr6:25395453..25397632,2	MCF-7	breast:
2	chr6:25387523..25389408-chr6:25391733..25393654,2	K562	blood:
3	chr6:25383605..25386265-chr6:25388595..25390846,2	K562	blood:

Variant related genes	Relation type
ENSG00000207490	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10498723	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10498724	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10946766	0.83[JPT][hapmap]
rs10946767	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946768	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524380	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12525031	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs12529416	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890508	1.00[CEU][hapmap]
rs16890520	1.00[CEU][hapmap]
rs16890531	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16890548	1.00[CEU][hapmap]
rs16890551	1.00[CEU][hapmap]
rs16890562	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs2149226	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2149228	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2149229	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2182932	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2182933	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2328881	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2328882	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4711083	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712925	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712926	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712927	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712928	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4712930	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4712931	0.92[JPT][hapmap]
rs55672111	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56248376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72830741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830745	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830747	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830750	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830753	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830754	0.90[ASN][1000 genomes]
rs72830758	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830759	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7751391	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7769124	1.00[CEU][hapmap]
rs926403	0.84[JPT][hapmap]
rs926404	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 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	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25377800-25395600	Weak transcription	Pancreas	Pancrea
3	chr6:25383000-25403600	Weak transcription	Right Atrium	heart
4	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:25384200-25391600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:25384800-25390600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:25385600-25390400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:25386400-25390800	Enhancers	Fetal Thymus	thymus
9	chr6:25387000-25389400	Enhancers	Thymus	Thymus
10	chr6:25387000-25389800	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:25387400-25389800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr6:25388200-25389800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:25388200-25390200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:25388200-25392800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr6:25388400-25389400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:25388400-25389600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:25388400-25390200	Enhancers	GM12878-XiMat	blood
18	chr6:25388400-25391600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:25388400-25392800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:25388400-25395800	Weak transcription	Primary T cells from cord blood	blood
21	chr6:25388400-25396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:25388400-25396000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:25388600-25389400	Enhancers	Primary B cells from cord blood	blood
24	chr6:25388600-25389600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:25388600-25389600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:25388600-25389800	Weak transcription	Brain Anterior Caudate	brain
27	chr6:25388800-25389400	Enhancers	NHEK	skin
28	chr6:25388800-25390200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:25388800-25390400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:25389000-25389400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:25389000-25390000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:25389000-25390400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr6:25389000-25391000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:25389200-25389400	Enhancers	H9 Cell Line	embryonic stem cell
35	chr6:25389200-25389600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:25389200-25389800	Enhancers	Left Ventricle	heart
37	chr6:25389200-25390400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:25389200-25390400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr6:25389200-25390400	Enhancers	HMEC	breast
40	chr6:25389200-25390400	Enhancers	NHDF-Ad	bronchial
41	chr6:25389200-25390800	Enhancers	Aorta	Aorta
42	chr6:25389200-25392800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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