Variant report

Variant	rs12424239
Chromosome Location	chr12:29715181-29715182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29713988..29716071-chr12:29717724..29720269,2	K562	blood:
2	chr12:29713752..29715262-chr12:29730590..29732837,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10492311	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11829731	0.83[EUR][1000 genomes]
rs11829994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11834102	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11834291	0.83[EUR][1000 genomes]
rs11837554	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12310251	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs12312423	1.00[CHB][hapmap]
rs12422557	1.00[CHB][hapmap]
rs12423770	1.00[CHB][hapmap]
rs12423941	1.00[CHB][hapmap]
rs12424502	1.00[CHB][hapmap]
rs12425004	1.00[CHB][hapmap]
rs12810686	1.00[CHB][hapmap]
rs12811228	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12813081	1.00[CHB][hapmap]
rs12816393	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12824107	1.00[CHB][hapmap]
rs12824420	1.00[CHB][hapmap]
rs12826187	1.00[CHB][hapmap]
rs12826210	1.00[CHB][hapmap]
rs12826633	1.00[CHB][hapmap]
rs12826893	0.87[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs142565	0.80[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs148897	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs159684	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs159688	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159691	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159692	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs159693	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16934448	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs16934474	0.88[CEU][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs16934556	0.88[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs1966531	0.82[JPT][hapmap]
rs2288228	0.88[CEU][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs299474	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs299477	0.80[CEU][hapmap]
rs299478	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299480	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299484	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299485	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34318689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825242	1.00[CHB][hapmap]
rs55793838	0.85[EUR][1000 genomes]
rs55970961	0.85[EUR][1000 genomes]
rs56255721	0.85[EUR][1000 genomes]
rs56367916	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56398900	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs57072643	0.83[EUR][1000 genomes]
rs57816450	0.89[EUR][1000 genomes]
rs58290227	0.93[EUR][1000 genomes]
rs59519970	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs59915017	0.85[EUR][1000 genomes]
rs60743264	0.85[EUR][1000 genomes]
rs7301943	0.85[EUR][1000 genomes]
rs73069592	0.89[EUR][1000 genomes]
rs73069593	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73069598	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73071505	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73071510	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73071517	0.97[EUR][1000 genomes]
rs73071519	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73071533	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73071556	0.94[EUR][1000 genomes]
rs73071582	0.93[EUR][1000 genomes]
rs7315541	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7316470	1.00[CHB][hapmap]
rs74078415	0.94[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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:29699400-29715800	Weak transcription	Right Ventricle	heart
4	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
6	chr12:29701200-29715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:29701200-29715600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:29703800-29715200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:29705000-29716000	Weak transcription	Spleen	Spleen
10	chr12:29706000-29715200	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:29706600-29716200	Weak transcription	Aorta	Aorta
12	chr12:29709800-29756200	Weak transcription	HMEC	breast
13	chr12:29710000-29715600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:29710200-29717800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:29711400-29716600	Enhancers	Stomach Mucosa	stomach
16	chr12:29711400-29718200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:29711800-29716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:29711800-29720800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:29712000-29715200	Weak transcription	Left Ventricle	heart
20	chr12:29712000-29715600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:29712600-29715200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:29712600-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:29712600-29715200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:29712600-29715600	Weak transcription	Right Atrium	heart
25	chr12:29712600-29722200	Weak transcription	Colonic Mucosa	Colon
26	chr12:29712600-29734600	Weak transcription	Liver	Liver
27	chr12:29712800-29722200	Weak transcription	Brain Germinal Matrix	brain
28	chr12:29713200-29719800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:29713200-29719800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:29713200-29726400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:29713200-29726600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:29713200-29731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:29714200-29715800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:29714200-29716200	Enhancers	HSMM	muscle
36	chr12:29714200-29716600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:29714200-29717400	Enhancers	Fetal Kidney	kidney
38	chr12:29714200-29717800	Enhancers	HSMMtube	muscle
39	chr12:29714400-29715400	Enhancers	Fetal Lung	lung
40	chr12:29714400-29716600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:29714400-29716600	Enhancers	NHDF-Ad	bronchial
42	chr12:29714400-29717400	Enhancers	Adipose Nuclei	Adipose
43	chr12:29714400-29717400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:29714400-29717600	Enhancers	NHLF	lung
45	chr12:29714400-29717800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:29714600-29715800	Weak transcription	Small Intestine	intestine
47	chr12:29714600-29717400	Enhancers	Fetal Heart	heart
48	chr12:29714800-29715200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:29714800-29715200	Flanking Active TSS	HUVEC	blood vessel
50	chr12:29715000-29715200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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