Variant report

Variant	rs2163972
Chromosome Location	chr3:85404960-85404961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11705775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491020	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs12493423	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs12498010	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12633910	0.85[CHD][hapmap]
rs12634949	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12714625	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076632	0.97[ASN][1000 genomes]
rs13085170	0.80[ASN][1000 genomes]
rs13099750	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1368737	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1368742	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1368743	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1433711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1821349	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs2117152	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2326313	0.80[ASN][1000 genomes]
rs3887151	0.93[ASN][1000 genomes]
rs4279114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4856269	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72615721	0.84[AMR][1000 genomes]
rs7627971	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9309977	0.86[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs9309981	0.82[MEX][hapmap]
rs9309982	0.82[MEX][hapmap]
rs9809258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9814919	0.80[ASN][1000 genomes]
rs9819830	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs9838811	0.82[MEX][hapmap]
rs986035	0.92[ASN][1000 genomes]
rs9861237	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9861451	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9865191	0.90[ASN][1000 genomes]
rs9879025	0.86[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs9880919	0.82[MEX][hapmap]
rs9990096	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1012601	chr3:85246185-85426996	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv536618	chr3:85246185-85426996	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv948806	chr3:85304744-85463443	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1013407	chr3:85307022-85460325	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
7	nsv870153	chr3:85326695-85426936	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1002238	chr3:85357855-85719373	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
9	nsv536619	chr3:85357855-85719373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1008956	chr3:85394816-85460325	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
11	nsv536620	chr3:85394816-85460325	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1004254	chr3:85394816-85514910	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
13	nsv536621	chr3:85394816-85514910	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85403800-85405200	Enhancers	Brain Anterior Caudate	brain
2	chr3:85404600-85405000	Active TSS	Brain Substantia Nigra	brain
3	chr3:85404600-85405200	Active TSS	Brain Angular Gyrus	brain
4	chr3:85404600-85405200	Active TSS	Brain Hippocampus Middle	brain
5	chr3:85404600-85410400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:85404800-85406000	Enhancers	Brain Cingulate Gyrus	brain

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