Variant report

Variant	rs12825680
Chromosome Location	chr12:39439630-39439631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10506132	0.84[EUR][1000 genomes]
rs10506135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169908	0.82[CEU][hapmap]
rs11608344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610886	0.81[EUR][1000 genomes]
rs11611172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612292	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613411	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809957	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810545	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812262	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs12813151	0.80[EUR][1000 genomes]
rs12815753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816546	0.81[EUR][1000 genomes]
rs12817946	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818844	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12827197	0.81[EUR][1000 genomes]
rs12827288	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12833449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349257	0.81[EUR][1000 genomes]
rs1562728	0.81[EUR][1000 genomes]
rs17126865	0.81[ASN][1000 genomes]
rs17465893	1.00[CHB][hapmap]
rs17467376	0.83[EUR][1000 genomes]
rs2218762	0.81[EUR][1000 genomes]
rs2388060	0.82[CEU][hapmap]
rs2388174	0.81[EUR][1000 genomes]
rs2388175	0.81[EUR][1000 genomes]
rs2388178	0.80[EUR][1000 genomes]
rs2388179	0.80[EUR][1000 genomes]
rs2388318	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2892450	0.80[EUR][1000 genomes]
rs2892451	0.80[EUR][1000 genomes]
rs34836816	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911962	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3914597	0.81[EUR][1000 genomes]
rs4254106	0.81[EUR][1000 genomes]
rs4411311	0.80[EUR][1000 genomes]
rs4438082	0.80[EUR][1000 genomes]
rs4768548	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]
rs7308161	0.80[EUR][1000 genomes]
rs7308278	0.80[EUR][1000 genomes]
rs7967776	0.82[CEU][hapmap]
rs7968566	0.80[EUR][1000 genomes]
rs7970850	0.81[EUR][1000 genomes]
rs7971416	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972629	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7976609	0.81[EUR][1000 genomes]
rs925827	0.80[EUR][1000 genomes]
rs925828	0.80[EUR][1000 genomes]
rs925829	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39437200-39452400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:39437600-39441200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:39437600-39441400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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