Variant report

Variant	rs9380865
Chromosome Location	chr6:39420954-39420955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39410899..39413477-chr6:39419818..39422781,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10947813	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11961693	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11962587	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11964924	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11968279	0.81[EUR][1000 genomes]
rs11968704	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11969059	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11969395	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12664369	0.81[EUR][1000 genomes]
rs1410488	0.89[ASN][1000 genomes]
rs16892158	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1927774	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1927775	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1952362	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2026670	0.89[CHB][hapmap]
rs2038198	0.81[EUR][1000 genomes]
rs2235817	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273063	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2395727	0.89[ASN][1000 genomes]
rs28533484	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35553201	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3736735	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs4236064	0.94[CHB][hapmap]
rs4464790	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482968	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4482969	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4540261	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs4605875	0.81[EUR][1000 genomes]
rs4711598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4714253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4714254	0.89[ASN][1000 genomes]
rs4714255	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714256	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs57703896	0.81[EUR][1000 genomes]
rs57799480	0.81[EUR][1000 genomes]
rs59617761	0.81[EUR][1000 genomes]
rs59724542	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72850669	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9296298	0.84[CHB][hapmap]
rs9296299	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296300	0.84[CHB][hapmap]
rs9349120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357305	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9357308	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357309	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9357311	0.81[EUR][1000 genomes]
rs9367008	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9367009	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9367012	0.83[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9367016	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9369117	0.88[ASN][1000 genomes]
rs9369119	0.84[CHB][hapmap]
rs9369123	0.81[EUR][1000 genomes]
rs9369124	0.81[ASN][1000 genomes]
rs9369126	0.81[EUR][1000 genomes]
rs9380861	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380862	0.89[ASN][1000 genomes]
rs9380863	0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9380864	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380867	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9380868	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9380871	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380872	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380873	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380877	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs9380879	0.81[EUR][1000 genomes]
rs9380880	0.81[EUR][1000 genomes]
rs9394592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9394594	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9394595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9394598	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9394599	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9394600	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394601	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394602	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9394603	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9394606	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs9394607	0.81[EUR][1000 genomes]
rs9394608	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs9394609	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs9394611	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs9394614	0.81[EUR][1000 genomes]
rs9471103	0.89[ASN][1000 genomes]
rs9471113	0.90[CHB][hapmap]

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	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv428145	chr6:39404129-39460795	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39418800-39421400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:39419200-39421400	Enhancers	NHDF-Ad	bronchial
3	chr6:39419200-39421800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:39419200-39421800	Enhancers	Fetal Stomach	stomach
5	chr6:39419400-39421400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:39419400-39421600	Enhancers	NHEK	skin
7	chr6:39419400-39421800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:39419400-39421800	Enhancers	HMEC	breast
9	chr6:39419600-39421600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:39420000-39421200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:39420000-39421200	Enhancers	NH-A	brain
12	chr6:39420000-39421800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:39420000-39422000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:39420200-39421000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:39420200-39421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:39420200-39421200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:39420200-39421200	Enhancers	Fetal Muscle Leg	muscle

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