Variant report

Variant	rs9822731
Chromosome Location	chr3:85405501-85405502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:85401815..85404016-chr3:85405205..85407101,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10154865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433498	0.82[EUR][1000 genomes]
rs11712915	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11713902	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11716233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11719276	0.81[ASN][1000 genomes]
rs12498010	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs12714629	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13068434	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13070166	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13076632	0.94[EUR][1000 genomes]
rs13076830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078384	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13085170	0.88[EUR][1000 genomes]
rs13099750	0.95[EUR][1000 genomes]
rs1368740	0.80[EUR][1000 genomes]
rs1368743	0.85[EUR][1000 genomes]
rs1433711	0.89[EUR][1000 genomes]
rs1449404	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1821349	0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2117151	0.81[CEU][hapmap]
rs2196096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2196097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2196098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2326313	0.85[EUR][1000 genomes]
rs4279114	0.88[EUR][1000 genomes]
rs6772991	0.85[EUR][1000 genomes]
rs6808159	0.84[EUR][1000 genomes]
rs6809805	0.87[AMR][1000 genomes]
rs71626887	0.84[EUR][1000 genomes]
rs7628948	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs7650834	0.84[EUR][1000 genomes]
rs9309977	0.85[EUR][1000 genomes]
rs9309981	0.85[TSI][hapmap]
rs9309982	0.86[TSI][hapmap]
rs9814516	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs9814919	0.88[EUR][1000 genomes]
rs9819830	0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs9820228	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9831374	0.81[ASN][1000 genomes]
rs9833314	0.84[EUR][1000 genomes]
rs9838811	0.83[TSI][hapmap]
rs9841144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9844512	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs9851444	0.88[CEU][hapmap]
rs9854869	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863620	0.83[EUR][1000 genomes]
rs9865191	0.88[EUR][1000 genomes]
rs9865745	0.84[EUR][1000 genomes]
rs9870448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873400	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9879025	0.85[EUR][1000 genomes]
rs9880397	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs9880919	0.88[TSI][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9822731	HTR1F	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85404600-85410400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:85404800-85406000	Enhancers	Brain Cingulate Gyrus	brain
3	chr3:85405000-85409800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:85405400-85405800	Enhancers	Brain Angular Gyrus	brain
5	chr3:85405400-85405800	Enhancers	Brain Hippocampus Middle	brain

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