Variant report

Variant	rs11638500
Chromosome Location	chr15:39949752-39949753
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39947922..39949877-chr15:39956880..39959494,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1004739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1004740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1004741	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10520135	0.87[CEU][hapmap]
rs10520137	1.00[CEU][hapmap]
rs11070220	0.89[CEU][hapmap]
rs11070222	1.00[CEU][hapmap]
rs11070223	0.88[CEU][hapmap]
rs11070225	0.89[CEU][hapmap]
rs1134485	1.00[CEU][hapmap]
rs11630406	0.89[CEU][hapmap]
rs11631570	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11632879	0.89[CEU][hapmap]
rs11633974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635103	0.89[CEU][hapmap]
rs11638041	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs11852591	0.89[CEU][hapmap]
rs11852649	0.89[CEU][hapmap]
rs11854797	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11856294	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856448	0.88[CHB][hapmap]
rs11856971	0.86[CEU][hapmap]
rs11857819	0.87[CEU][hapmap]
rs11857927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908846	1.00[CEU][hapmap]
rs12912082	1.00[CEU][hapmap]
rs16969386	1.00[CEU][hapmap]
rs16969410	0.89[CEU][hapmap]
rs16969445	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969459	0.89[CEU][hapmap]
rs16969460	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969475	1.00[CEU][hapmap]
rs16969478	1.00[CEU][hapmap]
rs16969495	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs16969637	0.89[CHB][hapmap]
rs16969640	0.89[CHB][hapmap]
rs1876853	1.00[CEU][hapmap]
rs2129458	0.81[EUR][1000 genomes]
rs2228261	1.00[CEU][hapmap]
rs2292304	0.83[JPT][hapmap]
rs2292305	1.00[CEU][hapmap]
rs2411312	0.92[EUR][1000 genomes]
rs2411313	0.89[CEU][hapmap]
rs2412409	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412410	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412411	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412413	1.00[CEU][hapmap]
rs2412415	0.89[CEU][hapmap]
rs2412417	0.89[CEU][hapmap]
rs2412419	1.00[CEU][hapmap]
rs2412424	0.81[EUR][1000 genomes]
rs2631708	0.81[EUR][1000 genomes]
rs2631709	0.81[EUR][1000 genomes]
rs2631712	0.81[EUR][1000 genomes]
rs2664124	0.81[EUR][1000 genomes]
rs2898686	0.89[CEU][hapmap]
rs2898687	1.00[CEU][hapmap]
rs2898688	0.89[CEU][hapmap]
rs34275067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754803	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784390	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs4349120	0.89[CEU][hapmap]
rs4476147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547308	0.89[CEU][hapmap]
rs4583211	0.88[CEU][hapmap]
rs56722485	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57969006	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58332880	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60884629	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7162070	1.00[CEU][hapmap]
rs7162781	1.00[CEU][hapmap]
rs7167184	1.00[CEU][hapmap]
rs7168755	0.89[CEU][hapmap]
rs7169478	1.00[CEU][hapmap]
rs7169574	0.89[CEU][hapmap]
rs72725045	0.81[EUR][1000 genomes]
rs753599	0.89[CEU][hapmap]
rs8029602	1.00[CEU][hapmap]
rs8032035	0.89[CEU][hapmap]
rs8035895	0.81[EUR][1000 genomes]
rs8036376	0.88[CEU][hapmap]
rs884584	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39938000-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:39938200-39950800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:39944800-39955600	Weak transcription	Fetal Lung	lung
5	chr15:39948400-39956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:39949000-39950400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr15:39949200-39950200	Enhancers	HSMM	muscle
8	chr15:39949200-39950200	Enhancers	NH-A	brain
9	chr15:39949200-39950200	Enhancers	NHDF-Ad	bronchial
10	chr15:39949200-39950400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:39949200-39950400	Enhancers	Osteobl	bone
12	chr15:39949200-39950800	Enhancers	HUVEC	blood vessel
13	chr15:39949400-39950000	Enhancers	NHLF	lung
14	chr15:39949400-39950400	Enhancers	Hela-S3	cervix
15	chr15:39949400-39954000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:39949400-39956200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:39949600-39950000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:39949600-39950200	Weak transcription	HSMMtube	muscle
19	chr15:39949600-39954000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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