Variant report

Variant	rs159692
Chromosome Location	chr12:29731948-29731949
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29713752..29715262-chr12:29730590..29732837,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10492311	0.89[EUR][1000 genomes]
rs11829731	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs11834102	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11834291	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs11837554	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12310251	0.84[EUR][1000 genomes]
rs12424239	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12822100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12826893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12826911	1.00[CHB][hapmap]
rs12828728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs142565	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs148897	0.91[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs159684	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs159688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159693	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934418	0.89[CHB][hapmap]
rs16934448	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs16934474	0.85[EUR][1000 genomes]
rs16934523	0.89[CHB][hapmap]
rs16934537	0.89[CHB][hapmap]
rs16934556	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs16934564	0.89[CHB][hapmap]
rs16934569	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16934597	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16934635	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2288228	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs299474	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299477	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs299478	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299480	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299482	0.89[CHB][hapmap]
rs299483	0.89[CHB][hapmap]
rs299484	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs299485	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34318689	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55807951	0.81[ASN][1000 genomes]
rs56367916	0.87[EUR][1000 genomes]
rs56398900	0.84[EUR][1000 genomes]
rs58290227	0.85[EUR][1000 genomes]
rs59519970	0.87[EUR][1000 genomes]
rs7301943	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73069598	0.83[EUR][1000 genomes]
rs73071505	0.89[EUR][1000 genomes]
rs73071510	0.89[EUR][1000 genomes]
rs73071517	0.84[EUR][1000 genomes]
rs73071519	0.84[EUR][1000 genomes]
rs73071533	0.84[EUR][1000 genomes]
rs73071556	0.87[EUR][1000 genomes]
rs73071582	0.85[EUR][1000 genomes]
rs7315541	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs74078415	0.87[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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
2	chr12:29709800-29756200	Weak transcription	HMEC	breast
3	chr12:29712600-29734600	Weak transcription	Liver	Liver
4	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:29717600-29734800	Weak transcription	NHLF	lung
7	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
8	chr12:29717800-29732200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:29720200-29735000	Weak transcription	NHDF-Ad	bronchial
10	chr12:29720200-29735800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:29720200-29743600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:29722400-29733600	Weak transcription	Ovary	ovary
13	chr12:29722400-29735400	Weak transcription	HSMMtube	muscle
14	chr12:29722600-29735200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:29722600-29736400	Weak transcription	Fetal Stomach	stomach
16	chr12:29722800-29735400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:29722800-29735800	Weak transcription	Fetal Kidney	kidney
18	chr12:29723000-29735200	Weak transcription	HSMM	muscle
19	chr12:29725600-29733400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:29725600-29735600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:29725800-29735200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:29726200-29734600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:29726200-29735200	Weak transcription	Aorta	Aorta
25	chr12:29727000-29735200	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:29727000-29735200	Weak transcription	Right Atrium	heart
27	chr12:29727200-29733800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:29727800-29735400	Weak transcription	Fetal Heart	heart
29	chr12:29728600-29733000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:29728600-29733600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:29728800-29735200	Weak transcription	Spleen	Spleen
32	chr12:29729000-29734000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:29729400-29744000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:29730200-29732200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:29730200-29732400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr12:29730200-29732600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:29730400-29732000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:29730400-29736200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:29730600-29732000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:29730600-29732800	Weak transcription	Left Ventricle	heart
41	chr12:29730600-29735600	Weak transcription	Right Ventricle	heart
42	chr12:29731000-29735200	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:29731000-29742600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:29731400-29732200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:29731400-29732400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:29731400-29735600	Weak transcription	Small Intestine	intestine
47	chr12:29731600-29732000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:29731800-29732000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:29731800-29733800	Weak transcription	Adipose Nuclei	Adipose
50	chr12:29731800-29733800	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links