Variant report

Variant	rs17129202
Chromosome Location	chr12:41682175-41682176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11180478	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180505	0.89[GIH][hapmap]
rs11180566	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180567	0.88[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180586	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180587	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180626	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180853	1.00[JPT][hapmap]
rs11180882	1.00[JPT][hapmap]
rs12296962	1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297017	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297322	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300590	0.90[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300840	0.82[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300884	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300953	0.89[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302094	0.89[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304516	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305252	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305924	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306285	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310793	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310860	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313636	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315362	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315979	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317394	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12427081	1.00[JPT][hapmap]
rs13377633	0.82[EUR][1000 genomes]
rs1367606	0.90[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431123	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431125	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431126	0.90[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589983	1.00[JPT][hapmap]
rs17129177	0.95[GIH][hapmap]
rs17129211	1.00[CEU][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]
rs1918231	1.00[JPT][hapmap]
rs2082222	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2217492	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405771	0.82[EUR][1000 genomes]
rs3858730	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768004	1.00[JPT][hapmap]
rs67832493	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73268788	0.95[EUR][1000 genomes]
rs73281725	0.84[EUR][1000 genomes]
rs7486754	1.00[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv469364	chr12:41631105-41710912	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv558699	chr12:41631105-41710912	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv558700	chr12:41665279-41710912	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41671200-41684600	Weak transcription	Ovary	ovary
2	chr12:41679800-41682600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr12:41680000-41682200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:41680000-41682400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:41680200-41682200	Enhancers	Fetal Lung	lung
6	chr12:41680400-41683600	Enhancers	Fetal Kidney	kidney
7	chr12:41680600-41688000	Weak transcription	Aorta	Aorta
8	chr12:41681000-41682200	Enhancers	Brain Hippocampus Middle	brain
9	chr12:41681000-41682600	Enhancers	Fetal Intestine Large	intestine
10	chr12:41681400-41682800	Enhancers	Brain Germinal Matrix	brain
11	chr12:41681600-41682200	Enhancers	Fetal Stomach	stomach
12	chr12:41681600-41682400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:41681800-41685800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:41682000-41682200	Enhancers	Colon Smooth Muscle	Colon
15	chr12:41682000-41682600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:41682000-41683200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:41682000-41683400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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