Variant report

Variant	rs3732799
Chromosome Location	chr3:113252042-113252043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113250521..113252326-chr3:113465017..113467077,2	MCF-7	breast:
2	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
3	chr20:61846286..61848363-chr3:113251582..113253331,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149658	Chromatin interaction
ENSG00000121579	Chromatin interaction
ENSG00000242659	Chromatin interaction
ENSG00000163611	Chromatin interaction
ENSG00000114573	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11914782	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs11919031	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs11922598	0.90[CEU][hapmap];0.82[MEX][hapmap]
rs11924017	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929418	0.81[JPT][hapmap]
rs12695292	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463641	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs16845107	0.83[GIH][hapmap]
rs16861025	0.84[JPT][hapmap]
rs16861032	0.84[JPT][hapmap]
rs16861130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861157	0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs16861165	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2007579	0.91[ASN][1000 genomes]
rs2254267	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399483	0.91[ASN][1000 genomes]
rs2399486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895414	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732807	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs3732808	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4331647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508746	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621301	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58686141	0.91[ASN][1000 genomes]
rs58884094	0.96[ASN][1000 genomes]
rs59631554	0.96[ASN][1000 genomes]
rs59666592	0.91[ASN][1000 genomes]
rs6764524	0.81[JPT][hapmap]
rs6766534	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769995	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771864	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782784	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6790846	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807610	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946779	0.91[ASN][1000 genomes]
rs72950827	0.96[ASN][1000 genomes]
rs7612047	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614678	0.81[JPT][hapmap]
rs7620700	0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs7623213	0.85[JPT][hapmap]
rs7636912	0.81[JPT][hapmap]
rs7636986	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs7646262	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs7650500	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs7653791	1.00[ASN][1000 genomes]
rs9682108	0.91[ASN][1000 genomes]
rs9848190	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854538	0.81[EUR][1000 genomes];1.00[ASN][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113250400-113252800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr3:113250400-113253200	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr3:113250600-113253200	Active TSS	Thymus	Thymus
4	chr3:113250600-113253400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:113250800-113252200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr3:113250800-113252400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
7	chr3:113250800-113253000	Active TSS	Duodenum Mucosa	Duodenum
8	chr3:113250800-113253000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
9	chr3:113250800-113253000	Bivalent/Poised TSS	A549	lung
10	chr3:113250800-113253200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:113250800-113253200	Active TSS	Rectal Smooth Muscle	rectum
12	chr3:113250800-113253200	Active TSS	Stomach Mucosa	stomach
13	chr3:113250800-113254600	Active TSS	GM12878-XiMat	blood
14	chr3:113251000-113252200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:113251000-113252200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:113251000-113252200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:113251000-113252200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:113251000-113252200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:113251000-113252200	Active TSS	Right Ventricle	heart
20	chr3:113251000-113252200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
21	chr3:113251000-113252400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr3:113251000-113252400	Active TSS	Primary B cells from peripheral blood	blood
23	chr3:113251000-113252400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr3:113251000-113252400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:113251000-113252400	Active TSS	Brain Angular Gyrus	brain
26	chr3:113251000-113252400	Active TSS	Fetal Thymus	thymus
27	chr3:113251000-113252400	Active TSS	Right Atrium	heart
28	chr3:113251000-113252400	Bivalent/Poised TSS	NHDF-Ad	bronchial
29	chr3:113251000-113252600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
30	chr3:113251000-113252600	Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr3:113251000-113252600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr3:113251000-113252600	Flanking Active TSS	Liver	Liver
33	chr3:113251000-113252600	Active TSS	Brain Substantia Nigra	brain
34	chr3:113251000-113252600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr3:113251000-113252600	Active TSS	Small Intestine	intestine
36	chr3:113251000-113252600	Flanking Bivalent TSS/Enh	NHEK	skin
37	chr3:113251000-113252800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:113251000-113252800	Active TSS	Primary T cells fromperipheralblood	blood
39	chr3:113251000-113252800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:113251000-113252800	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:113251000-113252800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:113251000-113252800	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:113251000-113252800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr3:113251000-113252800	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:113251000-113253200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr3:113251000-113253200	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:113251000-113253800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:113251200-113252200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr3:113251200-113252200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:113251200-113252200	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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