Variant report

Variant	rs12714143
Chromosome Location	chr2:85744885-85744886
allele	A/C
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	chr2:85741968..85744955-chr2:85763802..85767184,3	K562	blood:
4	chr2:85742777..85745374-chr2:85747062..85748764,2	MCF-7	breast:
5	chr2:85731450..85735055-chr2:85743773..85747296,3	K562	blood:
6	chr2:85743677..85746034-chr2:85749461..85751561,2	MCF-7	breast:
7	chr2:85739581..85746336-chr2:85762702..85767789,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10166612	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10167018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10172793	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174551	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10179904	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10187218	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	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]
rs10196357	1.00[ASN][1000 genomes]
rs10198001	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10198761	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10202828	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10496316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12714142	0.87[ASN][1000 genomes]
rs12714144	1.00[ASN][1000 genomes]
rs12714146	0.86[ASN][1000 genomes]
rs12714147	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12994163	0.92[CEU][hapmap];0.86[ASN][1000 genomes]
rs13000511	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13394092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13406611	1.00[ASN][1000 genomes]
rs13406935	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13408713	1.00[ASN][1000 genomes]
rs13409377	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13425821	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13431962	1.00[ASN][1000 genomes]
rs13432584	0.93[ASN][1000 genomes]
rs17430670	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17508809	1.00[CHB][hapmap]
rs17735885	0.96[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121397	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28398892	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479378	0.96[ASN][1000 genomes]
rs28564788	0.89[ASN][1000 genomes]
rs28800839	1.00[ASN][1000 genomes]
rs28810460	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212016	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34669893	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34824628	1.00[ASN][1000 genomes]
rs35776719	0.85[ASN][1000 genomes]
rs55892665	0.89[ASN][1000 genomes]
rs56359002	0.93[ASN][1000 genomes]
rs62165899	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62165905	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6727614	0.80[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12714143	GGCX	cis	Artery Aorta	GTEx
rs12714143	VAMP5	cis	lymphoblastoid	seeQTL
rs12714143	GGCX	cis	Artery Tibial	GTEx
rs12714143	GGCX	cis	Nerve Tibial	GTEx

Chromatin state (count:19 , 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	chr2:85742600-85745200	Enhancers	Fetal Intestine Large	intestine
5	chr2:85742800-85745200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr2:85743200-85745600	Enhancers	Stomach Mucosa	stomach
7	chr2:85743400-85745000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:85743800-85745000	Enhancers	Esophagus	oesophagus
9	chr2:85744000-85745000	Weak transcription	K562	blood
10	chr2:85744000-85750600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:85744200-85745000	Enhancers	Pancreas	Pancrea
12	chr2:85744200-85745000	Enhancers	Small Intestine	intestine
13	chr2:85744200-85745000	Bivalent Enhancer	HepG2	liver
14	chr2:85744400-85745200	Enhancers	Hela-S3	cervix
15	chr2:85744600-85745000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr2:85744600-85745200	Enhancers	A549	lung
17	chr2:85744600-85747400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:85744600-85750000	Weak transcription	Colonic Mucosa	Colon
19	chr2:85744600-85750200	Weak transcription	Fetal Intestine Small	intestine

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