Variant report

Variant	rs2196096
Chromosome Location	chr3:85470642-85470643
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	chr3:85468729..85471491-chr3:85479728..85483045,3	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10154865	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10433498	0.91[EUR][1000 genomes]
rs11127891	0.89[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];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498010	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs12633762	0.89[EUR][1000 genomes]
rs12714629	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13068434	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070166	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13076632	0.85[EUR][1000 genomes]
rs13076830	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13077660	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13084531	0.83[EUR][1000 genomes]
rs13085170	0.89[EUR][1000 genomes]
rs13099750	0.86[EUR][1000 genomes]
rs13353478	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1368739	0.89[EUR][1000 genomes]
rs1368740	0.89[EUR][1000 genomes]
rs1368743	0.91[EUR][1000 genomes]
rs1375547	0.89[GIH][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1433711	0.88[EUR][1000 genomes]
rs1449404	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1821349	0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2117151	0.81[CEU][hapmap]
rs2196097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326313	0.91[EUR][1000 genomes]
rs4279114	0.87[EUR][1000 genomes]
rs6772991	0.94[EUR][1000 genomes]
rs6808159	0.93[EUR][1000 genomes]
rs6809805	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71626887	0.92[EUR][1000 genomes]
rs7628948	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7650834	0.93[EUR][1000 genomes]
rs9309977	0.91[EUR][1000 genomes]
rs9309981	0.91[TSI][hapmap]
rs9309982	0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs9810724	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs9814516	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs9814919	0.89[EUR][1000 genomes]
rs9819830	0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs9820228	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9822731	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]
rs9826458	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9833314	0.92[EUR][1000 genomes]
rs9838811	0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs9841144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844512	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9851444	0.88[CEU][hapmap]
rs9854869	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9863620	0.91[EUR][1000 genomes]
rs9865191	0.87[EUR][1000 genomes]
rs9865745	0.93[EUR][1000 genomes]
rs9870448	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9873400	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9879025	0.91[EUR][1000 genomes]
rs9880397	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9880919	0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	nsv590904	chr3:85438564-85551403	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv590905	chr3:85438564-85797093	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv998829	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv536622	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv526621	chr3:85470642-85667683	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2196096	HTR1F	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85470200-85470800	Enhancers	Brain Germinal Matrix	brain
2	chr3:85470200-85471000	Enhancers	Fetal Brain Female	brain
3	chr3:85470400-85475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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