Variant report

Variant	rs28398892
Chromosome Location	chr2:85749918-85749919
allele	A/G
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	chr2:85747114..85750093-chr2:85750292..85751803,2	K562	blood:
4	chr2:85645966..85650126-chr2:85748875..85752927,8	MCF-7	breast:
5	chr2:85743677..85746034-chr2:85749461..85751561,2	MCF-7	breast:
6	chr2:85622932..85625793-chr2:85749685..85753171,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152292	Chromatin interaction
ENSG00000042493	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10166612	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10167018	0.96[ASN][1000 genomes]
rs10172793	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174551	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10179904	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187218	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10196357	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198001	0.87[ASN][1000 genomes]
rs10198761	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202828	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496316	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12714142	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12714143	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714144	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714146	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12714147	0.86[ASN][1000 genomes]
rs12994163	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000511	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.86[ASN][1000 genomes]
rs13394092	0.86[ASN][1000 genomes]
rs13406611	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406935	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408713	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409377	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425821	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	0.86[ASN][1000 genomes]
rs13431962	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432584	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17430670	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17735885	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121397	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28479378	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564788	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28800839	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28810460	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212016	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34565621	0.85[AMR][1000 genomes]
rs34669893	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824628	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776719	0.85[ASN][1000 genomes]
rs55892665	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56359002	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165899	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165905	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727614	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs28398892	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 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	chr2:85744600-85750000	Weak transcription	Colonic Mucosa	Colon
6	chr2:85744600-85750200	Weak transcription	Fetal Intestine Small	intestine
7	chr2:85745000-85750200	Weak transcription	Pancreas	Pancrea
8	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
9	chr2:85745200-85750200	Weak transcription	A549	lung
10	chr2:85745200-85750400	Weak transcription	Fetal Intestine Large	intestine
11	chr2:85745800-85750200	Weak transcription	K562	blood
12	chr2:85748400-85751000	Weak transcription	Psoas Muscle	Psoas
13	chr2:85748600-85751000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:85748800-85751800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:85749000-85751000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:85749400-85750600	Weak transcription	Small Intestine	intestine
17	chr2:85749400-85750600	Enhancers	Stomach Mucosa	stomach
18	chr2:85749400-85752600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:85749600-85750200	Weak transcription	Lung	lung
20	chr2:85749600-85750600	Weak transcription	NHDF-Ad	bronchial

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