Variant report

Variant	rs10190585
Chromosome Location	chr2:85746568-85746569
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	chr2:85739186..85748448-chr2:85762345..85768928,20	MCF-7	breast:
3	chr2:85731450..85735055-chr2:85743773..85747296,3	K562	blood:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10166612	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10167018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10172793	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10174551	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10179904	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10187218	0.89[ASN][1000 genomes]
rs10196357	0.96[ASN][1000 genomes]
rs10198001	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10198761	0.89[ASN][1000 genomes]
rs10202828	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10496316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714142	0.90[ASN][1000 genomes]
rs12714143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12714144	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12714146	0.83[ASN][1000 genomes]
rs12714147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12994163	0.92[CEU][hapmap];0.83[ASN][1000 genomes]
rs13000511	0.89[ASN][1000 genomes]
rs13387999	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13394092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13406611	0.96[ASN][1000 genomes]
rs13406935	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13408713	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13409377	0.89[ASN][1000 genomes]
rs13421434	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13425821	0.89[ASN][1000 genomes]
rs13426038	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13429968	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13431159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13431962	0.96[ASN][1000 genomes]
rs13432584	0.89[ASN][1000 genomes]
rs17430670	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17508727	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17508809	1.00[CHB][hapmap]
rs17735885	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2121397	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28398892	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28479378	0.93[ASN][1000 genomes]
rs28564788	0.86[ASN][1000 genomes]
rs28800839	0.96[ASN][1000 genomes]
rs28810460	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34212016	0.89[ASN][1000 genomes]
rs34214220	0.89[ASN][1000 genomes]
rs34669893	0.96[ASN][1000 genomes]
rs34824628	0.96[ASN][1000 genomes]
rs35776719	0.82[ASN][1000 genomes]
rs55892665	0.86[ASN][1000 genomes]
rs56359002	0.89[ASN][1000 genomes]
rs62165899	0.96[ASN][1000 genomes]
rs62165905	0.83[ASN][1000 genomes]
rs62165907	0.86[ASN][1000 genomes]
rs6727614	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7569073	1.00[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10190585	GGCX	cis	Nerve Tibial	GTEx
rs10190585	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 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	chr2:85744600-85747400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:85744600-85750000	Weak transcription	Colonic Mucosa	Colon
7	chr2:85744600-85750200	Weak transcription	Fetal Intestine Small	intestine
8	chr2:85745000-85750200	Weak transcription	Pancreas	Pancrea
9	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
10	chr2:85745200-85749400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:85745200-85750200	Weak transcription	A549	lung
12	chr2:85745200-85750400	Weak transcription	Fetal Intestine Large	intestine
13	chr2:85745600-85749400	Weak transcription	Stomach Mucosa	stomach
14	chr2:85745800-85750200	Weak transcription	K562	blood

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