Variant report

Variant	rs3856999
Chromosome Location	chr4:160784178-160784179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10031882	0.90[ASN][1000 genomes]
rs12643938	0.90[ASN][1000 genomes]
rs13103940	0.86[ASN][1000 genomes]
rs13124124	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13148410	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1457807	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17038961	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2137198	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348628	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2348634	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348635	0.89[EUR][1000 genomes]
rs2348987	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34487331	0.89[ASN][1000 genomes]
rs3846237	0.89[ASN][1000 genomes]
rs3856997	0.89[ASN][1000 genomes]
rs3911549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4034682	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4321587	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4563456	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4635771	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62333021	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62333023	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62333027	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62333043	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6833801	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6856039	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6856220	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6857955	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72980872	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733095	0.86[ASN][1000 genomes]
rs7688677	0.93[ASN][1000 genomes]
rs9995691	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015469	chr4:160389277-160841619	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537316	chr4:160389277-160841619	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv880358	chr4:160694415-161575183	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv595814	chr4:160705097-160834831	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv461696	chr4:160708061-160834831	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv595815	chr4:160708061-160834831	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1029076	chr4:160716044-160841619	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1030555	chr4:160731749-160793323	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv830130	chr4:160748243-160941680	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1027623	chr4:160758359-160837885	Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3856999	GRIA2	cis	parietal	SCAN
rs3856999	RAPGEF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160783000-160784200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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