Variant report

Variant	rs159699
Chromosome Location	chr12:29744208-29744209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10400534	0.83[JPT][hapmap]
rs10492312	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10771550	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10771551	0.87[ASN][1000 genomes]
rs10771552	0.85[ASN][1000 genomes]
rs10771553	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843445	0.84[ASN][1000 genomes]
rs11050285	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11050308	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12372765	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1409615	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs148898	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1529908	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs159685	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs159687	0.89[ASN][1000 genomes]
rs159689	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs159690	0.89[ASN][1000 genomes]
rs159694	0.88[ASN][1000 genomes]
rs159695	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs159697	0.89[ASN][1000 genomes]
rs159698	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs159700	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159712	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs159713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs159716	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs167253	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs177254	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1863224	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2081429	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2113879	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2113880	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs213539	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2148534	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2162033	0.86[ASN][1000 genomes]
rs2194819	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2209660	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2209661	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2209662	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2225065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2243623	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2254945	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2288230	0.86[ASN][1000 genomes]
rs2350532	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs2432958	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2710775	0.87[ASN][1000 genomes]
rs2766599	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2766600	0.87[ASN][1000 genomes]
rs2766601	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2766602	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2766604	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs299454	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs299462	0.90[CHB][hapmap]
rs299463	0.91[CHB][hapmap]
rs299465	0.91[CHB][hapmap]
rs299466	0.91[CHB][hapmap]
rs299467	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs299468	0.83[ASN][1000 genomes]
rs299470	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs299471	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs299472	0.86[CHB][hapmap]
rs299475	0.91[CHB][hapmap]
rs299479	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs299487	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs366998	0.80[ASN][1000 genomes]
rs3910440	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs3910441	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4931205	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57231427	0.87[ASN][1000 genomes]
rs7311193	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7959535	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7960236	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7960782	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7965227	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7976832	0.84[CEU][hapmap]
rs994171	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	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
6	nsv1051913	chr12:29741676-29770807	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 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	chr12:29709800-29756200	Weak transcription	HMEC	breast
2	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
5	chr12:29735400-29745800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:29736000-29752200	Weak transcription	HSMM	muscle
7	chr12:29736800-29762800	Weak transcription	Fetal Stomach	stomach
8	chr12:29737000-29748400	Weak transcription	Spleen	Spleen
9	chr12:29737200-29746800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:29737200-29748400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:29737200-29761800	Weak transcription	Right Ventricle	heart
12	chr12:29737200-29762400	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:29737200-29762800	Weak transcription	Psoas Muscle	Psoas
14	chr12:29741000-29748200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:29742200-29746000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:29742400-29744800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:29742600-29746200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:29742800-29750200	Weak transcription	Aorta	Aorta
19	chr12:29742800-29752200	Weak transcription	HSMMtube	muscle
20	chr12:29743200-29751800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:29743200-29769800	Weak transcription	NHLF	lung
22	chr12:29743400-29744400	Enhancers	Fetal Muscle Trunk	muscle
23	chr12:29743600-29744400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:29743600-29746200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr12:29743800-29745000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr12:29744000-29744400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr12:29744000-29744400	Enhancers	H9 Cell Line	embryonic stem cell
28	chr12:29744000-29744400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr12:29744000-29744400	Enhancers	Liver	Liver
30	chr12:29744000-29745000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:29744000-29745200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:29744000-29745200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:29744000-29746200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:29744200-29744400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:29744200-29744400	Enhancers	Lung	lung
36	chr12:29744200-29744400	Flanking Active TSS	Ovary	ovary
37	chr12:29744200-29744400	Active TSS	Osteobl	bone
38	chr12:29744200-29744600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:29744200-29744600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:29744200-29744600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:29744200-29744600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:29744200-29744600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:29744200-29744600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:29744200-29744600	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr12:29744200-29744600	Enhancers	Brain Anterior Caudate	brain
46	chr12:29744200-29744600	Enhancers	Brain Hippocampus Middle	brain
47	chr12:29744200-29744600	Enhancers	Fetal Muscle Leg	muscle
48	chr12:29744200-29744600	Genic enhancers	Left Ventricle	heart
49	chr12:29744200-29744600	Enhancers	Right Atrium	heart
50	chr12:29744200-29744600	Flanking Active TSS	NHDF-Ad	bronchial

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