Variant report

Variant	rs6795629
Chromosome Location	chr3:46149162-46149163
allele	C/T
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	chr3:46143235..46146105-chr3:46147610..46149596,2	MCF-7	breast:
3	chr3:46148102..46150678-chr3:46206152..46208391,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183625	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11130080	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11130085	0.90[ASN][1000 genomes]
rs11130086	0.91[ASN][1000 genomes]
rs1118879	0.86[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[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496322	0.90[ASN][1000 genomes]
rs12629632	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12630101	0.82[JPT][hapmap]
rs12635657	0.81[CHB][hapmap]
rs12637023	0.90[ASN][1000 genomes]
rs12639598	0.82[JPT][hapmap]
rs13060901	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs13065737	0.85[AMR][1000 genomes];0.84[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[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13098271	0.81[ASN][1000 genomes]
rs13434029	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13434336	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1392290	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs1491959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491960	0.81[JPT][hapmap]
rs1500005	0.81[ASN][1000 genomes]
rs1546077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546078	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602579	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1604069	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17078577	0.90[ASN][1000 genomes]
rs17078589	0.80[AFR][1000 genomes]
rs1909595	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1909596	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976366	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976367	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994490	0.81[JPT][hapmap]
rs2131091	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2201984	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2220678	0.92[ASN][1000 genomes]
rs2373150	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373151	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373153	0.90[ASN][1000 genomes]
rs2373154	0.95[CHB][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	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35435608	0.81[ASN][1000 genomes]
rs35462017	0.86[AMR][1000 genomes];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];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4314213	0.88[EUR][1000 genomes]
rs4318588	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4333119	0.81[ASN][1000 genomes]
rs4682806	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682809	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682810	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]
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	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61079448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441944	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764042	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs6776028	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780163	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6784214	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794103	0.90[ASN][1000 genomes]
rs6794475	0.90[ASN][1000 genomes]
rs6798934	0.93[YRI][hapmap]
rs6800484	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805094	0.80[EUR][1000 genomes]
rs6809381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[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	0.86[AMR][1000 genomes];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];0.86[JPT][hapmap]
rs7631598	0.82[ASN][1000 genomes]
rs7642701	0.81[ASN][1000 genomes]
rs9311386	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311387	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9637425	0.89[ASN][1000 genomes]
rs9814908	0.89[YRI][hapmap]
rs9824886	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9831926	0.90[YRI][hapmap]
rs9870445	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876587	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9990060	0.80[AFR][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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46129400-46154200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:46131400-46152200	Weak transcription	Pancreas	Pancrea
3	chr3:46139200-46150600	Weak transcription	Lung	lung
4	chr3:46140400-46149200	Weak transcription	NHLF	lung
5	chr3:46140400-46150000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:46140600-46150000	Weak transcription	Hela-S3	cervix
7	chr3:46140600-46150000	Weak transcription	HMEC	breast
8	chr3:46140800-46150000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:46141000-46150200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:46143200-46150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:46143800-46153000	Enhancers	Fetal Thymus	thymus
12	chr3:46144800-46149200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:46144800-46150600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:46145200-46152400	Enhancers	Dnd41	blood
15	chr3:46146200-46150200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:46146400-46150400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:46146400-46150600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:46146600-46150200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:46146800-46149200	Weak transcription	Placenta	Placenta
20	chr3:46146800-46164400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:46147200-46149600	Weak transcription	Primary B cells from cord blood	blood
22	chr3:46147200-46150600	Weak transcription	Primary T cells from cord blood	blood
23	chr3:46147400-46150400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:46147400-46150400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:46147400-46150400	Weak transcription	Spleen	Spleen
26	chr3:46147400-46150800	Weak transcription	Esophagus	oesophagus
27	chr3:46147600-46151400	Enhancers	Thymus	Thymus
28	chr3:46148200-46152800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:46148400-46160200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:46148600-46150000	Weak transcription	Fetal Lung	lung
31	chr3:46148600-46152800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr3:46148800-46151400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:46148800-46152800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:46149000-46150000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:46149000-46150600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:46149000-46151200	Enhancers	Small Intestine	intestine
37	chr3:46149000-46151600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr3:46149000-46152000	Enhancers	GM12878-XiMat	blood
39	chr3:46149000-46152000	Enhancers	Monocytes-CD14+_RO01746	blood

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