Variant report

Variant	rs62007455
Chromosome Location	chr15:62358479-62358480
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	chr15:62350853..62352703-chr15:62357418..62359025,2	K562	blood:

Variant related genes	Relation type
ENSG00000129003	Chromatin interaction
ENSG00000259251	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11634077	0.81[EUR][1000 genomes]
rs11634306	0.81[EUR][1000 genomes]
rs11634312	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11634818	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11637599	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11637693	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12148573	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12909386	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12909673	0.98[EUR][1000 genomes]
rs12911068	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911422	0.85[EUR][1000 genomes]
rs12913358	0.83[EUR][1000 genomes]
rs12917339	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17271312	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34311301	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34338090	0.98[EUR][1000 genomes]
rs34391931	1.00[EUR][1000 genomes]
rs34546531	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34933463	0.81[EUR][1000 genomes]
rs35119291	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35168171	0.90[EUR][1000 genomes]
rs35785804	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35932993	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36175042	0.81[EUR][1000 genomes]
rs62006969	0.81[EUR][1000 genomes]
rs62007448	0.84[EUR][1000 genomes]
rs62007453	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62007454	0.98[EUR][1000 genomes]
rs62008531	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62007455	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62353400-62358800	Weak transcription	Placenta	Placenta
2	chr15:62353400-62358800	Weak transcription	Psoas Muscle	Psoas
3	chr15:62353400-62358800	Weak transcription	Stomach Mucosa	stomach
4	chr15:62353400-62359000	Weak transcription	Lung	lung
5	chr15:62353600-62358600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:62353600-62358800	Weak transcription	Liver	Liver
7	chr15:62353600-62358800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:62353600-62358800	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:62353600-62358800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:62353800-62358800	Weak transcription	Adipose Nuclei	Adipose
11	chr15:62354000-62358600	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:62354000-62358800	Weak transcription	Brain Angular Gyrus	brain
13	chr15:62354200-62358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:62354200-62358800	Weak transcription	Brain Anterior Caudate	brain
15	chr15:62354400-62358600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:62354400-62358600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:62356200-62358800	Weak transcription	Esophagus	oesophagus
18	chr15:62356200-62358800	Weak transcription	Gastric	stomach
19	chr15:62356600-62360000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:62357000-62358800	Weak transcription	HUVEC	blood vessel
21	chr15:62357200-62358800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:62357200-62360400	Weak transcription	Hela-S3	cervix
23	chr15:62357400-62358800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:62357600-62358600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:62357600-62358800	Weak transcription	HMEC	breast
26	chr15:62358200-62358600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
27	chr15:62358200-62358800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr15:62358400-62358600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
29	chr15:62358400-62358600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr15:62358400-62358600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:62358400-62358600	Enhancers	Duodenum Mucosa	Duodenum
32	chr15:62358400-62358600	Bivalent Enhancer	Fetal Intestine Small	intestine
33	chr15:62358400-62358600	Enhancers	NHEK	skin
34	chr15:62358400-62358800	Enhancers	Aorta	Aorta
35	chr15:62358400-62358800	Enhancers	Colonic Mucosa	Colon
36	chr15:62358400-62358800	Bivalent Enhancer	Fetal Intestine Large	intestine
37	chr15:62358400-62358800	Enhancers	Pancreas	Pancrea
38	chr15:62358400-62358800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
39	chr15:62358400-62359000	Enhancers	Left Ventricle	heart
40	chr15:62358400-62359600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links