Variant report

Variant	rs2406862
Chromosome Location	chr12:43006387-43006388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10736003	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785356	0.97[EUR][1000 genomes]
rs10785358	1.00[EUR][1000 genomes]
rs10880331	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12422484	0.82[EUR][1000 genomes]
rs12423337	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12423346	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12423349	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12423470	0.82[EUR][1000 genomes]
rs12423824	0.82[EUR][1000 genomes]
rs12424138	0.88[EUR][1000 genomes]
rs12424455	0.88[EUR][1000 genomes]
rs12424504	0.88[EUR][1000 genomes]
rs12424511	0.88[EUR][1000 genomes]
rs12424763	0.88[EUR][1000 genomes]
rs12424886	0.88[EUR][1000 genomes]
rs12425177	0.88[EUR][1000 genomes]
rs12425193	0.88[EUR][1000 genomes]
rs12425470	1.00[CEU][hapmap]
rs12425775	0.88[EUR][1000 genomes]
rs12426290	0.88[EUR][1000 genomes]
rs12426303	0.88[EUR][1000 genomes]
rs12426479	0.82[EUR][1000 genomes]
rs12426718	0.82[EUR][1000 genomes]
rs12426988	0.88[EUR][1000 genomes]
rs12827135	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17091490	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17091505	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1922756	0.88[EUR][1000 genomes]
rs2178751	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2406858	0.88[EUR][1000 genomes]
rs2406861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897539	0.88[EUR][1000 genomes]
rs4238085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4590936	0.88[EUR][1000 genomes]
rs4768425	0.97[EUR][1000 genomes]
rs57263961	0.82[EUR][1000 genomes]
rs57908879	0.88[EUR][1000 genomes]
rs60211398	0.88[EUR][1000 genomes]
rs60776045	0.82[EUR][1000 genomes]
rs7131974	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs7133039	0.88[EUR][1000 genomes]
rs7133172	0.88[EUR][1000 genomes]
rs7133774	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs7295407	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7296915	0.82[EUR][1000 genomes]
rs7301558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303511	0.82[EUR][1000 genomes]
rs7304849	0.88[EUR][1000 genomes]
rs7306530	0.82[EUR][1000 genomes]
rs7306683	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7307159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7314565	0.88[EUR][1000 genomes]
rs7952819	1.00[EUR][1000 genomes]
rs7959843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964774	1.00[EUR][1000 genomes]
rs7976696	0.88[EUR][1000 genomes]
rs9988993	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv832389	chr12:43003361-43173896	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv2761736	chr12:43005994-43012946	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43002800-43007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:43005000-43006800	Enhancers	Fetal Muscle Leg	muscle
3	chr12:43005200-43007400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:43005400-43006400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:43005400-43006400	Enhancers	NHDF-Ad	bronchial
6	chr12:43005400-43006600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:43005400-43006600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:43005400-43006800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:43005400-43006800	Enhancers	Adipose Nuclei	Adipose
10	chr12:43005600-43006400	Enhancers	Colon Smooth Muscle	Colon
11	chr12:43005600-43006400	Enhancers	Fetal Kidney	kidney
12	chr12:43005600-43006600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:43005600-43006800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:43005800-43006400	Enhancers	Stomach Smooth Muscle	stomach
15	chr12:43006000-43007000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:43006000-43007600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:43006000-43015800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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