Variant report

Variant	rs4682810
Chromosome Location	chr3:46152501-46152502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46148560..46157677-chr3:46203034..46208483,12	MCF-7	breast:
2	chr3:46152200..46152791-chr3:46204079..46204942,2	MCF-7	breast:
3	chr3:46150790..46153435-chr3:46242926..46245585,2	MCF-7	breast:
4	chr3:46129568..46133226-chr3:46150928..46153874,4	MCF-7	breast:
5	chr3:46130825..46132979-chr3:46149857..46153032,4	MCF-7	breast:
6	chr3:46149777..46152755-chr3:46160739..46163366,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183625	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11130080	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11130085	0.90[ASN][1000 genomes]
rs11130086	0.91[ASN][1000 genomes]
rs1118879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917890	0.90[ASN][1000 genomes]
rs11929281	0.90[ASN][1000 genomes]
rs12485978	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496322	0.90[ASN][1000 genomes]
rs12629632	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12630101	0.82[JPT][hapmap]
rs12635657	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs12637023	0.90[ASN][1000 genomes]
rs12639598	0.82[JPT][hapmap]
rs13060901	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs13065737	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13073861	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs13077099	0.90[ASN][1000 genomes]
rs13077923	0.92[ASN][1000 genomes]
rs13078053	0.93[ASN][1000 genomes]
rs13082280	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13098271	0.81[ASN][1000 genomes]
rs13434029	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13434336	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1392290	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1491959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491960	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1500005	0.81[ASN][1000 genomes]
rs1546077	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602579	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1604069	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17078577	0.90[ASN][1000 genomes]
rs1909595	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1909596	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976366	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976367	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994490	0.82[JPT][hapmap]
rs2131091	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2201984	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2220678	0.92[ASN][1000 genomes]
rs2373150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373151	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373153	0.90[ASN][1000 genomes]
rs2373154	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs34067839	0.92[ASN][1000 genomes]
rs34381514	0.81[ASN][1000 genomes]
rs34906043	0.81[ASN][1000 genomes]
rs35359253	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35435608	0.81[ASN][1000 genomes]
rs35462017	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35567508	0.93[ASN][1000 genomes]
rs35657218	0.81[ASN][1000 genomes]
rs36111470	0.92[ASN][1000 genomes]
rs3733100	0.82[JPT][hapmap]
rs3796375	0.82[JPT][hapmap]
rs3821884	0.82[JPT][hapmap]
rs3851347	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4314213	0.88[EUR][1000 genomes]
rs4318588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4333119	0.81[ASN][1000 genomes]
rs4682806	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682809	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683168	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683175	0.90[ASN][1000 genomes]
rs4683178	0.90[ASN][1000 genomes]
rs56307311	0.92[ASN][1000 genomes]
rs59521415	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61079448	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764042	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6776028	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780163	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs6784214	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794103	0.90[ASN][1000 genomes]
rs6794475	0.90[ASN][1000 genomes]
rs6795629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800484	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805094	0.81[EUR][1000 genomes]
rs6809381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs730983	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs737452	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs751552	0.82[JPT][hapmap]
rs751553	0.82[JPT][hapmap]
rs7610518	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7616464	0.81[ASN][1000 genomes]
rs7623460	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs7631598	0.82[ASN][1000 genomes]
rs7642701	0.81[ASN][1000 genomes]
rs9311386	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311387	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9637425	0.89[ASN][1000 genomes]
rs9824886	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849015	0.80[EUR][1000 genomes]
rs9870445	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876587	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9990063	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46129400-46154200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:46143800-46153000	Enhancers	Fetal Thymus	thymus
3	chr3:46146800-46164400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:46148200-46152800	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr3:46148400-46160200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:46148600-46152800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:46148800-46152800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:46149200-46158800	Enhancers	NHLF	lung
9	chr3:46149200-46159800	Enhancers	Placenta	Placenta
10	chr3:46149400-46152800	Enhancers	HSMM	muscle
11	chr3:46149600-46152600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:46150000-46153000	Enhancers	Fetal Lung	lung
13	chr3:46150000-46157600	Enhancers	HMEC	breast
14	chr3:46150200-46152600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:46150400-46158800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:46150600-46153000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:46150600-46158600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:46150800-46154000	Weak transcription	HSMMtube	muscle
19	chr3:46151000-46155800	Weak transcription	Liver	Liver
20	chr3:46151000-46158800	Weak transcription	Stomach Mucosa	stomach
21	chr3:46151200-46153000	Enhancers	Adipose Nuclei	Adipose
22	chr3:46151200-46153800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:46151200-46154200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:46151200-46156400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:46151400-46156000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:46151600-46154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:46151800-46153000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:46151800-46153000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:46151800-46158200	Enhancers	NHDF-Ad	bronchial
30	chr3:46152000-46152600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr3:46152000-46152600	Flanking Active TSS	GM12878-XiMat	blood
32	chr3:46152000-46152800	Enhancers	Brain Germinal Matrix	brain
33	chr3:46152000-46152800	Enhancers	Colon Smooth Muscle	Colon
34	chr3:46152000-46152800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr3:46152000-46152800	Enhancers	NH-A	brain
36	chr3:46152000-46157400	Enhancers	NHEK	skin
37	chr3:46152200-46152600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:46152200-46152600	Enhancers	Fetal Stomach	stomach
39	chr3:46152200-46152600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr3:46152200-46152600	Enhancers	Spleen	Spleen
41	chr3:46152200-46152800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:46152200-46152800	Enhancers	H9 Cell Line	embryonic stem cell
43	chr3:46152200-46152800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:46152200-46152800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr3:46152200-46152800	Enhancers	Esophagus	oesophagus
46	chr3:46152200-46152800	Enhancers	Lung	lung
47	chr3:46152200-46152800	Enhancers	Pancreas	Pancrea
48	chr3:46152200-46152800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:46152200-46153000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:46152200-46153000	Active TSS	Rectal Mucosa Donor 29	rectum

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