Variant report

Variant	rs12486784
Chromosome Location	chr3:85304744-85304745
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10440085	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11127880	0.82[CHB][hapmap]
rs11127882	1.00[CHB][hapmap]
rs11127883	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127884	1.00[CHB][hapmap]
rs12053927	1.00[CHB][hapmap]
rs12486846	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs12487792	0.90[CEU][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs12488308	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13061527	0.82[CHB][hapmap]
rs1349602	1.00[CHB][hapmap]
rs1376936	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1376938	1.00[CHB][hapmap]
rs1452122	1.00[CHB][hapmap]
rs1452123	1.00[CHB][hapmap]
rs1452126	1.00[CHB][hapmap]
rs1452127	1.00[CHB][hapmap]
rs1545926	0.82[CHB][hapmap]
rs1839938	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968691	1.00[CHB][hapmap]
rs1985716	0.85[ASN][1000 genomes]
rs2034619	1.00[CHB][hapmap]
rs2167606	1.00[CHB][hapmap]
rs2171141	0.89[CHD][hapmap]
rs2220244	0.82[CHB][hapmap]
rs2290339	1.00[CHB][hapmap]
rs58013523	0.90[ASN][1000 genomes]
rs58223718	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59880141	0.88[ASN][1000 genomes]
rs6775792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6780644	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6789415	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6796256	0.82[CHB][hapmap]
rs6799730	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909180	0.92[ASN][1000 genomes]
rs7623714	0.82[CHB][hapmap]
rs7630177	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7632628	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[YRI][hapmap]
rs7635613	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636138	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs7637876	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap]
rs7637886	0.89[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap]
rs7642449	0.87[ASN][1000 genomes]
rs818214	0.86[ASN][1000 genomes]
rs818216	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs818217	1.00[CHB][hapmap]
rs818218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs818220	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs818221	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs818222	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs818226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9309970	0.82[CHB][hapmap]
rs9681960	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9810830	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap]
rs9813787	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9818067	1.00[CHB][hapmap]
rs9819278	0.82[CHB][hapmap]
rs9820587	0.82[CHB][hapmap]
rs9832814	0.88[ASN][1000 genomes]
rs9866167	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875381	0.82[CHB][hapmap]
rs9882148	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap]
rs9882296	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883252	0.82[CHB][hapmap]
rs994237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	nsv877096	chr3:85163167-85366517	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv460747	chr3:85163167-85391672	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590899	chr3:85163167-85391672	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1001124	chr3:85167047-85309046	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv877098	chr3:85177173-85361645	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv470716	chr3:85194054-85316648	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv590903	chr3:85200742-85316648	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv999255	chr3:85222822-85323285	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv536617	chr3:85222822-85323285	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv877100	chr3:85234199-85336559	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1006718	chr3:85243599-85323285	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1012601	chr3:85246185-85426996	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv536618	chr3:85246185-85426996	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	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

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85288400-85307600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85303000-85308200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:85303600-85305400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:85304200-85305200	Enhancers	Brain Hippocampus Middle	brain
5	chr3:85304200-85305200	Weak transcription	Brain Substantia Nigra	brain
6	chr3:85304200-85307200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:85304400-85307600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:85304600-85307200	Weak transcription	Brain Angular Gyrus	brain

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