Variant report

Variant	rs299456
Chromosome Location	chr12:29695861-29695862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10400534	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10400541	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10492312	0.84[EUR][1000 genomes]
rs10771545	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10771546	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs10771547	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs10771549	0.93[ASN][1000 genomes]
rs10771550	0.89[EUR][1000 genomes]
rs10771551	0.89[EUR][1000 genomes]
rs10771552	0.86[EUR][1000 genomes]
rs10843443	0.91[ASN][1000 genomes]
rs10843445	0.87[EUR][1000 genomes]
rs10843446	0.84[ASN][1000 genomes]
rs11050270	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11050271	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11050273	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11050278	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050280	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050281	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050284	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050285	0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs11050288	0.84[ASN][1000 genomes]
rs11050291	0.84[ASN][1000 genomes]
rs11050292	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs11050293	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11050295	0.84[ASN][1000 genomes]
rs11050296	0.84[ASN][1000 genomes]
rs11050297	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11050299	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11050300	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11050301	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11050302	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs11050308	0.87[EUR][1000 genomes]
rs11611194	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12371221	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12579805	0.81[CHB][hapmap]
rs12581671	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12810291	0.84[ASN][1000 genomes]
rs12820673	0.83[ASN][1000 genomes]
rs1326758	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1409616	0.81[CHB][hapmap]
rs148898	0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs1529908	0.87[EUR][1000 genomes]
rs159685	0.87[EUR][1000 genomes]
rs159687	0.87[EUR][1000 genomes]
rs159689	0.87[EUR][1000 genomes]
rs159690	0.88[EUR][1000 genomes]
rs159694	0.83[EUR][1000 genomes]
rs159695	0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs159696	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159697	0.87[EUR][1000 genomes]
rs159698	0.87[EUR][1000 genomes]
rs159701	0.90[CHB][hapmap]
rs159703	0.95[CHB][hapmap]
rs159704	0.90[CHB][hapmap]
rs159705	0.90[CHB][hapmap]
rs159707	0.86[CHB][hapmap]
rs159708	0.86[CHB][hapmap]
rs159714	0.81[CHB][hapmap]
rs177254	0.87[EUR][1000 genomes]
rs1988548	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2060569	0.93[ASN][1000 genomes]
rs2081429	0.87[EUR][1000 genomes]
rs2162033	0.87[EUR][1000 genomes]
rs2194819	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs2243623	0.87[EUR][1000 genomes]
rs2254945	0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs2288131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288132	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2288133	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2553077	0.82[CHB][hapmap]
rs2710775	0.83[EUR][1000 genomes]
rs2766599	0.88[EUR][1000 genomes]
rs2766600	0.87[EUR][1000 genomes]
rs2766601	0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs2766602	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2766604	0.87[EUR][1000 genomes]
rs2766605	0.81[CHB][hapmap]
rs2766606	0.82[CHB][hapmap]
rs299444	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299445	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299453	0.97[EUR][1000 genomes]
rs299454	0.86[JPT][hapmap];0.97[EUR][1000 genomes]
rs299455	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs299457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299459	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299467	0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs299468	0.91[EUR][1000 genomes]
rs299470	0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs299471	0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs299479	0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs299487	0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs34020170	0.82[ASN][1000 genomes]
rs34187264	0.82[ASN][1000 genomes]
rs34555972	0.87[ASN][1000 genomes]
rs35111056	0.91[ASN][1000 genomes]
rs35536095	0.84[ASN][1000 genomes]
rs35741143	0.90[ASN][1000 genomes]
rs366998	0.96[EUR][1000 genomes]
rs375109	0.93[ASN][1000 genomes]
rs3910440	0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3910441	0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4931201	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4931204	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57231427	0.88[EUR][1000 genomes]
rs60500145	0.84[ASN][1000 genomes]
rs6487837	0.88[ASN][1000 genomes]
rs7294502	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs7295284	0.81[CHB][hapmap]
rs7301491	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7306397	0.93[ASN][1000 genomes]
rs7310555	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs7310895	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs7311193	0.86[EUR][1000 genomes]
rs7314549	0.94[CHB][hapmap];0.91[ASN][1000 genomes]
rs7971202	0.93[ASN][1000 genomes]
rs9300191	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs9300192	0.88[ASN][1000 genomes]
rs9738399	0.81[ASN][1000 genomes]
rs994172	0.82[CHB][hapmap]

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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29650400-29699000	Weak transcription	Right Ventricle	heart
2	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:29668800-29706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:29670600-29697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:29670600-29699000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:29671000-29697200	Weak transcription	Spleen	Spleen
8	chr12:29671600-29697200	Weak transcription	Left Ventricle	heart
9	chr12:29673600-29708800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:29682200-29697400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:29687800-29696000	Weak transcription	HSMM	muscle
12	chr12:29688200-29699000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:29688200-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:29689400-29700000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:29690800-29696000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:29690800-29696600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:29691000-29705800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:29691200-29698800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:29691200-29709200	Weak transcription	HMEC	breast
20	chr12:29693000-29705600	Weak transcription	Hela-S3	cervix
21	chr12:29695400-29696000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:29695400-29696000	Enhancers	NHDF-Ad	bronchial
23	chr12:29695400-29696400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:29695400-29697400	Enhancers	Fetal Stomach	stomach
25	chr12:29695600-29696200	Enhancers	NHLF	lung
26	chr12:29695600-29697000	Enhancers	Fetal Brain Male	brain
27	chr12:29695800-29696000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:29695800-29696200	Enhancers	Fetal Lung	lung
29	chr12:29695800-29696200	Enhancers	Stomach Smooth Muscle	stomach
30	chr12:29695800-29696400	Active TSS	Aorta	Aorta
31	chr12:29695800-29696400	Active TSS	Ovary	ovary
32	chr12:29695800-29696600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr12:29695800-29696800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:29695800-29696800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:29695800-29697200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:29695800-29697200	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:29695800-29698000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:29695800-29699000	Weak transcription	Psoas Muscle	Psoas

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