Variant report

Variant	rs2163970
Chromosome Location	chr3:85446451-85446452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1014796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs1030720	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10433499	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10511078	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10865609	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs10865611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11127885	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11127898	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11714549	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs12054328	1.00[JPT][hapmap]
rs12487446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12491707	1.00[JPT][hapmap]
rs12492753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12494446	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12497411	1.00[MEX][hapmap]
rs12498133	1.00[JPT][hapmap]
rs12629607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12631046	0.82[ASN][1000 genomes]
rs12631345	1.00[ASN][1000 genomes]
rs12638798	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12639001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12639564	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1368744	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1368746	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1368747	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1375566	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1433710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1433712	0.97[ASN][1000 genomes]
rs1433713	0.88[ASN][1000 genomes]
rs1449386	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1449403	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1465716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MKK][hapmap];0.94[ASN][1000 genomes]
rs1594795	0.88[ASN][1000 genomes]
rs17023019	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs17023032	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1821350	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1836131	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897698	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900916	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1992967	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2017293	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap]
rs2018416	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2044725	1.00[JPT][hapmap]
rs2053105	1.00[ASN][1000 genomes]
rs2077839	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2167043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2326319	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2875907	1.00[CHD][hapmap]
rs4856270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856274	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4856568	1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856582	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4856584	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62250710	0.82[ASN][1000 genomes]
rs6549027	0.82[ASN][1000 genomes]
rs6762253	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771447	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772750	0.90[ASN][1000 genomes]
rs6778223	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6781515	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap]
rs6807666	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6809486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6810225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs726610	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs734298	0.82[ASN][1000 genomes]
rs7610238	1.00[ASN][1000 genomes]
rs7618494	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7623369	0.88[ASN][1000 genomes]
rs7623474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7623947	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7640828	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7647981	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7651113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7652808	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs892365	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9309974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9309975	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9309976	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9309978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9824071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9824386	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9824840	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9825345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9830359	0.82[ASN][1000 genomes]
rs9831848	0.82[ASN][1000 genomes]
rs9833972	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9843953	0.82[ASN][1000 genomes]
rs9846153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9847998	0.81[ASW][hapmap];0.83[LWK][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap]
rs9854888	0.94[ASN][1000 genomes]
rs9866182	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873752	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9879417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs989534	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9990095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv590904	chr3:85438564-85551403	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	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

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85416200-85450200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85446400-85446600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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