Variant report

Variant	rs970280
Chromosome Location	chr15:39864403-39864404
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	chr15:39858767..39865533-chr15:39870539..39876162,6	MCF-7	breast:
2	chr15:39861270..39862826-chr15:39863131..39865842,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10152640	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10520138	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11070220	0.80[ASN][1000 genomes]
rs1134485	0.83[ASN][1000 genomes]
rs12443011	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12910572	0.81[ASN][1000 genomes]
rs12912082	0.85[ASN][1000 genomes]
rs1478604	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1478605	0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1904209	0.80[ASN][1000 genomes]
rs2169830	0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2292305	0.86[ASN][1000 genomes]
rs2618162	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2618163	0.84[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2664139	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2664141	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167366	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7170682	0.84[ASN][1000 genomes]
rs7179293	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7183544	0.84[ASN][1000 genomes]
rs753599	0.83[ASN][1000 genomes]
rs8034594	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8036376	0.84[ASN][1000 genomes]
rs8036633	0.84[ASN][1000 genomes]
rs8039035	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs949646	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs964424	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39851000-39871800	Weak transcription	Pancreas	Pancrea
2	chr15:39854400-39870800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:39857800-39870600	Weak transcription	HSMMtube	muscle
4	chr15:39862600-39865600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:39863200-39865400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:39863600-39865600	Weak transcription	Fetal Lung	lung
7	chr15:39863600-39871200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:39864000-39865000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links