Variant report

Variant	rs28479378
Chromosome Location	chr2:85750407-85750408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85744073..85747943-chr2:85749869..85754586,8	K562	blood:
2	chr2:85741540..85743418-chr2:85749217..85750940,2	MCF-7	breast:
3	chr2:85645966..85650126-chr2:85748875..85752927,8	MCF-7	breast:
4	chr2:85743677..85746034-chr2:85749461..85751561,2	MCF-7	breast:
5	chr2:85747114..85750093-chr2:85750292..85751803,2	K562	blood:
6	chr2:85622932..85625793-chr2:85749685..85753171,3	MCF-7	breast:
7	chr2:85663235..85666181-chr2:85750315..85752072,2	K562	blood:

Variant related genes	Relation type
ENSG00000042493	Chromatin interaction
ENSG00000152292	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10166612	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10167018	0.93[ASN][1000 genomes]
rs10172793	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10174551	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10179904	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187218	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190585	0.93[ASN][1000 genomes]
rs10196357	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10198001	0.84[ASN][1000 genomes]
rs10198761	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10202828	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10496316	0.93[ASN][1000 genomes]
rs12714142	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12714143	0.96[ASN][1000 genomes]
rs12714144	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12714146	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12714147	0.82[ASN][1000 genomes]
rs12994163	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13000511	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13387999	0.82[ASN][1000 genomes]
rs13394092	0.82[ASN][1000 genomes]
rs13406611	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13406935	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13408713	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13409377	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13421434	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13425821	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13426038	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429968	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13431159	0.82[ASN][1000 genomes]
rs13431962	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13432584	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17430670	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17508727	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17735885	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2121397	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28398892	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564788	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28800839	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28810460	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34212016	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34214220	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34669893	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34824628	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35776719	0.82[ASN][1000 genomes]
rs55892665	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56359002	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62165899	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62165905	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62165907	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6727614	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28479378	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85733600-85750600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:85734600-85750800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:85744000-85750600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
6	chr2:85748400-85751000	Weak transcription	Psoas Muscle	Psoas
7	chr2:85748600-85751000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:85748800-85751800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:85749000-85751000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:85749400-85750600	Weak transcription	Small Intestine	intestine
11	chr2:85749400-85750600	Enhancers	Stomach Mucosa	stomach
12	chr2:85749400-85752600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr2:85749600-85750600	Weak transcription	NHDF-Ad	bronchial
14	chr2:85750000-85752600	Enhancers	Colonic Mucosa	Colon
15	chr2:85750200-85751000	Enhancers	Pancreas	Pancrea
16	chr2:85750200-85751200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr2:85750200-85751800	Bivalent Enhancer	HepG2	liver
18	chr2:85750200-85751800	Enhancers	K562	blood
19	chr2:85750200-85752400	Enhancers	A549	lung
20	chr2:85750200-85752600	Enhancers	Lung	lung
21	chr2:85750200-85753000	Enhancers	Fetal Intestine Small	intestine
22	chr2:85750200-85753000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr2:85750400-85750600	Enhancers	Stomach Smooth Muscle	stomach
24	chr2:85750400-85752000	Enhancers	Gastric	stomach
25	chr2:85750400-85752600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:85750400-85752600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:85750400-85752600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:85750400-85752800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:85750400-85752800	Enhancers	Brain Anterior Caudate	brain
30	chr2:85750400-85752800	Enhancers	Brain Hippocampus Middle	brain
31	chr2:85750400-85752800	Enhancers	Fetal Intestine Large	intestine
32	chr2:85750400-85752800	Enhancers	Fetal Stomach	stomach
33	chr2:85750400-85752800	Enhancers	Left Ventricle	heart
34	chr2:85750400-85753000	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:85750400-85753000	Enhancers	Duodenum Mucosa	Duodenum
36	chr2:85750400-85753000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:85750400-85754600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links