Variant report

Variant	rs62002378
Chromosome Location	chr15:39805096-39805097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39802198..39806304-chr15:39871801..39874775,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10152903	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152951	1.00[ASN][1000 genomes]
rs1038097	1.00[ASN][1000 genomes]
rs1051442	1.00[ASN][1000 genomes]
rs12438058	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442155	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442221	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379938	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1382443	1.00[ASN][1000 genomes]
rs1382444	1.00[ASN][1000 genomes]
rs16969143	1.00[ASN][1000 genomes]
rs16969167	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17631807	1.00[ASN][1000 genomes]
rs17633107	1.00[ASN][1000 genomes]
rs17633210	1.00[ASN][1000 genomes]
rs17702987	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705806	1.00[ASN][1000 genomes]
rs17706179	1.00[ASN][1000 genomes]
rs1813493	1.00[ASN][1000 genomes]
rs2228262	1.00[ASN][1000 genomes]
rs2228263	1.00[ASN][1000 genomes]
rs2618156	1.00[ASN][1000 genomes]
rs2618161	1.00[ASN][1000 genomes]
rs2618166	1.00[ASN][1000 genomes]
rs2618167	1.00[ASN][1000 genomes]
rs2664123	1.00[ASN][1000 genomes]
rs2664137	1.00[ASN][1000 genomes]
rs28622135	1.00[ASN][1000 genomes]
rs35275624	1.00[ASN][1000 genomes]
rs41315060	1.00[ASN][1000 genomes]
rs4923835	1.00[ASN][1000 genomes]
rs58188999	1.00[ASN][1000 genomes]
rs62002368	1.00[ASN][1000 genomes]
rs62002377	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002379	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002380	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002384	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179604	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008647	1.00[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39802000-39805200	Enhancers	K562	blood
2	chr15:39802000-39806000	Enhancers	Fetal Muscle Leg	muscle
3	chr15:39802200-39805200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr15:39802800-39805400	Enhancers	Fetal Heart	heart
5	chr15:39803400-39805200	Enhancers	Colonic Mucosa	Colon
6	chr15:39803400-39805400	Enhancers	Fetal Stomach	stomach
7	chr15:39803600-39805200	Enhancers	Fetal Muscle Trunk	muscle
8	chr15:39804000-39805200	Enhancers	Duodenum Mucosa	Duodenum
9	chr15:39804200-39805200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:39804200-39805200	Enhancers	NHDF-Ad	bronchial
11	chr15:39804200-39811000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:39804400-39805200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:39804400-39805200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:39804400-39805600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:39804800-39805200	Enhancers	Fetal Thymus	thymus
16	chr15:39804800-39805200	Enhancers	Thymus	Thymus
17	chr15:39805000-39806000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links