Variant report

Variant	rs12643676
Chromosome Location	chr4:93527004-93527005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10516908	0.81[AMR][1000 genomes]
rs10516909	0.85[AMR][1000 genomes]
rs12643027	0.81[AMR][1000 genomes]
rs12650228	0.85[AMR][1000 genomes]
rs13103135	0.81[AMR][1000 genomes]
rs13103707	0.81[AMR][1000 genomes]
rs13108903	0.81[AMR][1000 genomes]
rs13116623	0.85[AMR][1000 genomes]
rs13130344	0.81[AMR][1000 genomes]
rs13145212	0.81[AMR][1000 genomes]
rs13146517	0.81[AMR][1000 genomes]
rs13149456	0.81[AMR][1000 genomes]
rs1479324	0.85[EUR][1000 genomes]
rs1585761	0.86[EUR][1000 genomes]
rs1600319	0.94[EUR][1000 genomes]
rs17019443	0.81[AMR][1000 genomes]
rs17019446	0.81[AMR][1000 genomes]
rs17019461	0.81[AMR][1000 genomes]
rs17019529	0.81[AMR][1000 genomes]
rs17019548	0.81[AMR][1000 genomes]
rs17019565	0.82[AMR][1000 genomes]
rs17019576	0.85[AMR][1000 genomes]
rs17019587	0.80[AMR][1000 genomes]
rs17019598	0.81[AMR][1000 genomes]
rs17019702	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17019739	0.94[EUR][1000 genomes]
rs1993030	0.81[AMR][1000 genomes]
rs2060676	0.81[AMR][1000 genomes]
rs2060677	0.85[AMR][1000 genomes]
rs2122522	0.81[AMR][1000 genomes]
rs2122523	0.85[AMR][1000 genomes]
rs34154904	0.81[AMR][1000 genomes]
rs34340904	0.92[EUR][1000 genomes]
rs34529116	0.85[AMR][1000 genomes]
rs34566524	0.85[AMR][1000 genomes]
rs34660259	0.81[AMR][1000 genomes]
rs34867192	0.85[AMR][1000 genomes]
rs34971193	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35012816	0.82[AMR][1000 genomes]
rs35177691	0.85[AMR][1000 genomes]
rs35186291	0.85[AMR][1000 genomes]
rs35981540	0.85[AMR][1000 genomes]
rs36065598	0.81[AMR][1000 genomes]
rs62307818	0.81[AMR][1000 genomes]
rs62307918	0.96[EUR][1000 genomes]
rs62310084	0.85[AMR][1000 genomes]
rs6532379	0.85[EUR][1000 genomes]
rs66507847	0.81[AMR][1000 genomes]
rs6844431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72661970	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7654414	0.87[EUR][1000 genomes]
rs7659771	0.83[AMR][1000 genomes]
rs7676091	0.81[EUR][1000 genomes]
rs7681873	0.85[AMR][1000 genomes]
rs7681890	0.87[EUR][1000 genomes]
rs7694867	0.84[EUR][1000 genomes]
rs921355	0.96[EUR][1000 genomes]
rs922514	0.81[EUR][1000 genomes]
rs930676	0.85[AMR][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	nsv948712	chr4:93007985-93740409	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1005500	chr4:93359923-93590452	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv537184	chr4:93359923-93590452	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv879605	chr4:93376231-93740409	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1014431	chr4:93464326-93618241	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv537185	chr4:93464326-93618241	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv879608	chr4:93480717-93612903	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv879609	chr4:93489287-93596167	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv830008	chr4:93510957-93685935	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12643676	GRID2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:93495600-93535600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:93496400-93540200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:93502800-93531400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:93510800-93539600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:93522600-93534000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:93523800-93531400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:93524200-93539400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:93524600-93530400	Weak transcription	H1 Cell Line	embryonic stem cell

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