Variant report

Variant	rs7668740
Chromosome Location	chr4:93539532-93539533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10012693	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11097346	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11934648	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11937751	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12641482	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12643761	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119028	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13142861	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13143245	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1450502	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1479325	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1479333	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1600320	0.91[ASN][1000 genomes]
rs17842180	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2169945	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2870640	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2870641	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34464836	0.86[EUR][1000 genomes]
rs34905965	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35266197	0.86[EUR][1000 genomes]
rs57939475	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532378	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812161	0.80[ASN][1000 genomes]
rs6832010	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6832040	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7672511	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899469	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs970405	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9968392	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7668740	GRID2	cis	parietal	SCAN
rs7668740	ATOH1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:93496400-93540200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:93510800-93539600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:93529000-93540400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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