Variant report

Variant	rs28538495
Chromosome Location	chr15:40059180-40059181
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	chr15:40058706..40061655-chr15:40069031..40071989,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1021410	0.88[ASN][1000 genomes]
rs1027232	0.85[ASN][1000 genomes]
rs11858148	0.96[ASN][1000 genomes]
rs12437837	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12440567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491624	0.83[ASN][1000 genomes]
rs1565559	0.81[ASN][1000 genomes]
rs1565561	0.80[ASN][1000 genomes]
rs16969789	0.94[ASN][1000 genomes]
rs16969802	0.94[ASN][1000 genomes]
rs16969808	0.86[AFR][1000 genomes]
rs16969811	0.86[AFR][1000 genomes]
rs16969823	0.85[AFR][1000 genomes]
rs1844863	0.85[ASN][1000 genomes]
rs1906166	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2029584	0.83[ASN][1000 genomes]
rs2171312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450006	0.84[ASN][1000 genomes]
rs28861150	0.90[AFR][1000 genomes]
rs28884199	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28896916	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34320375	0.85[ASN][1000 genomes]
rs35652496	0.83[ASN][1000 genomes]
rs41424848	0.88[AFR][1000 genomes]
rs4924387	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924388	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924390	0.85[ASN][1000 genomes]
rs4924392	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58312028	0.85[ASN][1000 genomes]
rs59434895	0.96[ASN][1000 genomes]
rs60431166	0.96[ASN][1000 genomes]
rs61695850	0.96[ASN][1000 genomes]
rs62004808	0.85[ASN][1000 genomes]
rs7179742	0.85[ASN][1000 genomes]
rs7179838	0.85[ASN][1000 genomes]
rs7180846	0.85[ASN][1000 genomes]
rs72727079	0.86[AFR][1000 genomes]
rs72727081	0.86[AFR][1000 genomes]
rs72727083	0.86[AFR][1000 genomes]
rs72727084	0.86[AFR][1000 genomes]
rs72727092	0.88[AFR][1000 genomes]
rs73397133	0.85[ASN][1000 genomes]
rs8026892	0.81[ASN][1000 genomes]
rs8035291	0.83[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	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
2	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
3	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40040800-40063400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:40052200-40063600	Weak transcription	Brain Angular Gyrus	brain
3	chr15:40053400-40069400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:40054400-40069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:40054600-40059800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:40054600-40062800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:40056200-40063000	Weak transcription	Esophagus	oesophagus
8	chr15:40058200-40063000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:40058200-40063200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:40059000-40063000	Weak transcription	Right Atrium	heart

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