Variant report

Variant	rs11856294
Chromosome Location	chr15:39924486-39924487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39871401..39883645-chr15:39918779..39926575,24	MCF-7	breast:
2	chr15:39901531..39904246-chr15:39922575..39924532,2	MCF-7	breast:
3	chr15:39923096..39925308-chr15:39927555..39929722,2	K562	blood:
4	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
5	chr15:39884563..39886445-chr15:39923081..39926308,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction
ENSG00000259279	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1004739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004741	1.00[EUR][1000 genomes];1.00[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]
rs11632879	0.89[CEU][hapmap]
rs11633974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11635103	0.89[CEU][hapmap]
rs11638041	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11638500	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]
rs11852591	0.89[CEU][hapmap]
rs11852649	0.89[CEU][hapmap]
rs11854797	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs11856448	0.88[CHB][hapmap]
rs11856971	0.86[CEU][hapmap]
rs11857819	0.87[CEU][hapmap]
rs11857927	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[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];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969459	0.89[CEU][hapmap]
rs16969460	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969475	1.00[CEU][hapmap]
rs16969478	1.00[CEU][hapmap]
rs16969495	0.84[CHB][hapmap]
rs16969637	0.89[CHB][hapmap]
rs16969640	0.89[CHB][hapmap]
rs1876853	1.00[CEU][hapmap]
rs2228261	1.00[CEU][hapmap]
rs2292304	0.83[JPT][hapmap]
rs2292305	1.00[CEU][hapmap]
rs2411312	0.84[EUR][1000 genomes]
rs2411313	0.89[CEU][hapmap]
rs2412409	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412410	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412411	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412413	1.00[CEU][hapmap]
rs2412415	0.89[CEU][hapmap]
rs2412417	0.89[CEU][hapmap]
rs2412419	1.00[CEU][hapmap]
rs2898686	0.89[CEU][hapmap]
rs2898687	1.00[CEU][hapmap]
rs2898688	0.89[CEU][hapmap]
rs34275067	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35754803	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784390	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4349120	0.89[CEU][hapmap]
rs4476147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547308	0.89[CEU][hapmap]
rs4583211	0.88[CEU][hapmap]
rs56722485	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57969006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58332880	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60884629	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs753599	0.89[CEU][hapmap]
rs8029602	1.00[CEU][hapmap]
rs8032035	0.89[CEU][hapmap]
rs8036376	0.88[CEU][hapmap]
rs884584	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:39917600-39926200	Weak transcription	Esophagus	oesophagus
3	chr15:39920800-39925200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:39921400-39926200	Weak transcription	Pancreas	Pancrea
5	chr15:39921400-39937600	Weak transcription	Psoas Muscle	Psoas
6	chr15:39923600-39925400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:39923800-39926200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:39923800-39939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:39924200-39932200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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