Variant report

Variant	rs16863250
Chromosome Location	chr3:150934109-150934110
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	chr3:150919820..150922068-chr3:150933502..150935019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174946	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12106682	1.00[EUR][1000 genomes]
rs12631155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12633262	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12633553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12636713	0.81[AFR][1000 genomes]
rs12637362	0.81[ASN][1000 genomes]
rs12638293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1431496	0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs16863151	1.00[CHB][hapmap]
rs16863173	1.00[EUR][1000 genomes]
rs16863208	0.81[YRI][hapmap]
rs16863219	1.00[EUR][1000 genomes]
rs16863248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2060080	0.89[ASN][1000 genomes]
rs2870413	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs2870414	0.92[AFR][1000 genomes]
rs2870415	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773614	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs3773618	0.89[ASN][1000 genomes]
rs3821666	1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3960212	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41526246	1.00[EUR][1000 genomes]
rs41526349	1.00[EUR][1000 genomes]
rs58321514	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60620665	1.00[EUR][1000 genomes]
rs60816259	1.00[EUR][1000 genomes]
rs60966250	1.00[EUR][1000 genomes]
rs6440723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440725	1.00[EUR][1000 genomes]
rs66725169	0.92[AFR][1000 genomes]
rs6767615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67740545	0.92[AFR][1000 genomes]
rs6774659	1.00[EUR][1000 genomes]
rs6776934	1.00[EUR][1000 genomes]
rs6777211	1.00[EUR][1000 genomes]
rs6787551	1.00[EUR][1000 genomes]
rs6790244	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6790349	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794447	1.00[EUR][1000 genomes]
rs6806896	0.81[ASN][1000 genomes]
rs73009177	1.00[EUR][1000 genomes]
rs73012977	1.00[EUR][1000 genomes]
rs73012978	1.00[EUR][1000 genomes]
rs73012986	1.00[EUR][1000 genomes]
rs73012988	1.00[EUR][1000 genomes]
rs73012992	1.00[EUR][1000 genomes]
rs73013000	1.00[EUR][1000 genomes]
rs73014806	1.00[EUR][1000 genomes]
rs73014871	1.00[EUR][1000 genomes]
rs73014873	1.00[EUR][1000 genomes]
rs73016712	1.00[EUR][1000 genomes]
rs73016789	1.00[EUR][1000 genomes]
rs73018604	0.81[AFR][1000 genomes]
rs73018620	1.00[EUR][1000 genomes]
rs73019085	0.83[AFR][1000 genomes]
rs73019093	1.00[EUR][1000 genomes]
rs73019099	1.00[EUR][1000 genomes]
rs73021108	1.00[EUR][1000 genomes]
rs73021116	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73021122	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73021129	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73021144	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73155774	0.81[ASN][1000 genomes]
rs7616375	0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs7618087	1.00[EUR][1000 genomes]
rs7638986	1.00[EUR][1000 genomes]
rs7653225	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
2	chr3:150928200-150936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:150928800-150943800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:150928800-150946200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:150928800-150952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:150928800-150953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:150929000-150934400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:150929000-150935000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:150929000-150938200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:150929000-150943200	Weak transcription	Psoas Muscle	Psoas
11	chr3:150929000-150945200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:150929200-150935000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:150929200-150938000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:150929200-150945400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:150929600-150934200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:150929600-150939200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:150929800-150935200	Weak transcription	Liver	Liver
18	chr3:150931400-150936000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:150932200-150934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:150932200-150935000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:150932200-150936800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:150932200-150942800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:150932400-150937400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:150932400-150938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:150932600-150934400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:150932600-150946200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:150933200-150935600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:150933400-150934400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:150933400-150937200	Strong transcription	Primary B cells from cord blood	blood
30	chr3:150933400-150937600	Enhancers	NHDF-Ad	bronchial
31	chr3:150933400-150937800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:150933600-150934400	Enhancers	Fetal Heart	heart
33	chr3:150933600-150935400	Enhancers	Adipose Nuclei	Adipose
34	chr3:150933600-150937200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:150933600-150937400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:150933600-150937600	Enhancers	NH-A	brain
37	chr3:150933600-150937600	Enhancers	NHLF	lung
38	chr3:150933800-150934200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:150933800-150934600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:150933800-150935000	Weak transcription	Left Ventricle	heart
41	chr3:150933800-150936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:150934000-150935400	Enhancers	Brain Anterior Caudate	brain

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