Variant report

Variant	rs336574
Chromosome Location	chr3:161067350-161067351
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	chr3:160992668..160995441-chr3:161067329..161069400,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12488318	0.86[ASN][1000 genomes]
rs12494261	0.87[ASN][1000 genomes]
rs12494844	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs13318781	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs1450519	0.83[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs1471440	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs1478567	0.87[ASN][1000 genomes]
rs163138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336544	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs336545	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs336546	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs336564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs336571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs336573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336576	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336581	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419703	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4429651	0.80[ASN][1000 genomes]
rs4487256	1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4490410	0.94[CHB][hapmap]
rs455739	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs458197	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs459067	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs461616	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs462081	0.95[ASN][1000 genomes]
rs57201455	0.92[ASN][1000 genomes]
rs62279860	0.80[ASN][1000 genomes]
rs62279861	0.80[ASN][1000 genomes]
rs73160362	0.80[ASN][1000 genomes]
rs73162530	0.92[ASN][1000 genomes]
rs9290072	0.88[CEU][hapmap];0.87[CHB][hapmap]
rs9290075	0.86[ASN][1000 genomes]
rs978933	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9811833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9812083	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs9825118	0.94[CHB][hapmap]
rs9827833	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9828189	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs9828231	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs9836094	0.80[ASN][1000 genomes]
rs9839404	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs9859045	0.87[ASN][1000 genomes]
rs9876553	0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.82[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
4	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161058200-161072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:161060600-161070200	Weak transcription	Esophagus	oesophagus
4	chr3:161062200-161067400	Weak transcription	Gastric	stomach
5	chr3:161062600-161067600	Weak transcription	HepG2	liver
6	chr3:161064400-161083000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:161065400-161069200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:161065600-161068200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:161065600-161069000	Enhancers	NHDF-Ad	bronchial
10	chr3:161065800-161068200	Enhancers	Osteobl	bone
11	chr3:161065800-161068800	Enhancers	NH-A	brain
12	chr3:161065800-161069000	Enhancers	HMEC	breast
13	chr3:161065800-161069200	Enhancers	NHEK	skin
14	chr3:161065800-161069600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:161066000-161068800	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr3:161066200-161067400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:161066200-161068400	Enhancers	Stomach Mucosa	stomach
18	chr3:161066200-161068600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:161066200-161069400	Enhancers	Hela-S3	cervix
20	chr3:161066400-161068200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:161066600-161068800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:161066600-161069200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:161066800-161067600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:161066800-161068200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:161066800-161068400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr3:161066800-161068600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:161066800-161068600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:161066800-161068600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:161066800-161068600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:161066800-161068800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:161067000-161067600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:161067000-161068400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:161067000-161068600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:161067000-161068800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:161067000-161069400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:161067200-161068000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:161067200-161068200	Bivalent Enhancer	Dnd41	blood
38	chr3:161067200-161068200	Enhancers	NHLF	lung
39	chr3:161067200-161068400	Enhancers	Primary T cells from cord blood	blood
40	chr3:161067200-161069000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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