Variant report

Variant	rs12497257
Chromosome Location	chr3:61211945-61211946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10510864	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130825	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707666	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11711696	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486043	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487887	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12488069	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494967	0.82[CEU][hapmap]
rs12495661	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12498118	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12633494	0.82[CEU][hapmap]
rs1453741	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1524018	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17064628	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17064657	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17064663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17064715	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1851784	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34371746	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4458366	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4688353	0.89[EUR][1000 genomes]
rs60559507	0.84[EUR][1000 genomes]
rs6799813	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs879365	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839448	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839707	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9871848	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9880846	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv997718	chr3:61176349-61222975	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61201200-61221000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61203200-61215400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:61203200-61222200	Weak transcription	Psoas Muscle	Psoas
4	chr3:61203400-61213400	Weak transcription	Fetal Lung	lung
5	chr3:61203400-61225600	Weak transcription	Lung	lung
6	chr3:61203400-61225600	Weak transcription	Pancreas	Pancrea
7	chr3:61207200-61219400	Weak transcription	GM12878-XiMat	blood
8	chr3:61208000-61213400	Weak transcription	Fetal Stomach	stomach
9	chr3:61208000-61225600	Weak transcription	Right Atrium	heart
10	chr3:61208200-61212000	Weak transcription	Spleen	Spleen
11	chr3:61208200-61217800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:61208400-61219800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:61209400-61219400	Weak transcription	Ovary	ovary
14	chr3:61209800-61212000	Weak transcription	Brain Substantia Nigra	brain
15	chr3:61210600-61213400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:61211400-61212000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr3:61211400-61212800	Enhancers	Fetal Brain Male	brain
18	chr3:61211800-61212000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:61211800-61212000	Enhancers	Fetal Brain Female	brain
20	chr3:61211800-61212000	Enhancers	Left Ventricle	heart
21	chr3:61211800-61212200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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