Variant report

Variant	rs10400534
Chromosome Location	chr12:29719953-29719954
allele	A/G
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:

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10400541	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10492312	0.90[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10771545	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs10771546	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs10771547	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs10771549	0.82[ASN][1000 genomes]
rs10771550	0.95[CEU][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771551	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771552	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10843443	0.80[ASN][1000 genomes]
rs10843445	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10843446	0.87[ASN][1000 genomes]
rs11050270	0.94[CHB][hapmap]
rs11050271	0.95[CHB][hapmap]
rs11050273	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs11050278	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050280	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050281	0.84[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050284	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050285	1.00[CEU][hapmap];0.88[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11050288	0.89[ASN][1000 genomes]
rs11050291	0.89[ASN][1000 genomes]
rs11050292	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs11050293	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs11050295	0.89[ASN][1000 genomes]
rs11050296	0.89[ASN][1000 genomes]
rs11050297	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050298	0.92[ASN][1000 genomes]
rs11050299	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050300	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050301	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050302	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs11050308	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11611194	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs12371221	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs12372765	0.83[JPT][hapmap]
rs12581671	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs12810291	0.89[ASN][1000 genomes]
rs12820673	0.91[ASN][1000 genomes]
rs1326758	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1409615	0.83[JPT][hapmap]
rs148898	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1529908	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs159685	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs159687	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs159689	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs159690	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159694	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs159695	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs159696	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs159697	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs159698	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs159699	0.83[JPT][hapmap]
rs159700	0.83[JPT][hapmap]
rs159701	0.89[CHB][hapmap]
rs159703	0.89[CHB][hapmap]
rs159704	0.89[CHB][hapmap]
rs159705	0.89[CHB][hapmap]
rs159707	0.84[CHB][hapmap]
rs159708	0.84[CHB][hapmap]
rs159709	0.85[CHB][hapmap]
rs159713	0.82[JPT][hapmap]
rs159716	0.83[JPT][hapmap]
rs177254	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1863224	0.83[JPT][hapmap]
rs1988548	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs2060569	0.82[ASN][1000 genomes]
rs2081429	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2162033	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2194819	1.00[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2209660	0.83[JPT][hapmap]
rs2209661	0.82[JPT][hapmap]
rs2209662	0.83[JPT][hapmap]
rs2225065	0.80[JPT][hapmap]
rs2243623	0.89[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2254945	1.00[CEU][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2288131	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2288132	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs2288133	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs2710775	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2766599	0.89[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2766600	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2766601	1.00[CEU][hapmap];0.88[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2766602	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2766604	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs299444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299453	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299454	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299455	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs299456	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs299457	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs299459	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs299467	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs299468	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs299469	0.84[AMR][1000 genomes]
rs299470	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs299471	0.90[CEU][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs299479	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs299487	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34020170	0.87[ASN][1000 genomes]
rs34187264	0.87[ASN][1000 genomes]
rs34555972	0.87[ASN][1000 genomes]
rs35111056	0.80[ASN][1000 genomes]
rs35536095	0.87[ASN][1000 genomes]
rs366998	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs375109	0.82[ASN][1000 genomes]
rs3910440	0.86[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs3910441	0.85[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs4931201	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs4931204	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57231427	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60500145	0.87[ASN][1000 genomes]
rs6487837	0.86[ASN][1000 genomes]
rs7294502	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs7301491	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs7306397	0.82[ASN][1000 genomes]
rs7310555	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs7310895	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs7311193	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7314549	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs7959535	0.82[JPT][hapmap]
rs7960782	0.83[JPT][hapmap]
rs7965227	0.82[JPT][hapmap]
rs7971202	0.82[ASN][1000 genomes]
rs9300191	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9300192	0.86[ASN][1000 genomes]
rs9738399	0.85[ASN][1000 genomes]
rs994171	0.83[JPT][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:66 , 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	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
3	chr12:29709800-29756200	Weak transcription	HMEC	breast
4	chr12:29711800-29720800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:29712600-29722200	Weak transcription	Colonic Mucosa	Colon
6	chr12:29712600-29734600	Weak transcription	Liver	Liver
7	chr12:29712800-29722200	Weak transcription	Brain Germinal Matrix	brain
8	chr12:29713200-29726400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:29713200-29726600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:29713200-29731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:29715400-29721400	Weak transcription	Esophagus	oesophagus
13	chr12:29715400-29722200	Weak transcription	Fetal Lung	lung
14	chr12:29715400-29731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:29715800-29724800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:29716400-29721000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:29716400-29722200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:29717000-29720000	Weak transcription	Right Atrium	heart
20	chr12:29717000-29721800	Weak transcription	HUVEC	blood vessel
21	chr12:29717400-29720400	Weak transcription	Fetal Heart	heart
22	chr12:29717400-29722200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:29717600-29721600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:29717600-29721600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:29717600-29725000	Weak transcription	Aorta	Aorta
26	chr12:29717600-29727400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:29717600-29727800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:29717600-29734800	Weak transcription	NHLF	lung
29	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
30	chr12:29717800-29721600	Weak transcription	HSMMtube	muscle
31	chr12:29717800-29732200	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:29718000-29720000	Weak transcription	Hela-S3	cervix
33	chr12:29718000-29720200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:29718200-29720000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:29718200-29725400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:29718600-29727600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:29718800-29720200	Enhancers	Ovary	ovary
38	chr12:29718800-29723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:29719000-29720000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:29719000-29720000	Genic enhancers	Left Ventricle	heart
41	chr12:29719000-29720000	Enhancers	Lung	lung
42	chr12:29719000-29720000	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr12:29719000-29720200	Enhancers	Gastric	stomach
44	chr12:29719200-29720000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:29719200-29720000	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr12:29719200-29720200	Enhancers	Adipose Nuclei	Adipose
47	chr12:29719200-29721800	Weak transcription	HSMM	muscle
48	chr12:29719400-29720000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:29719400-29720200	Enhancers	Fetal Muscle Trunk	muscle
50	chr12:29719400-29720200	Enhancers	Osteobl	bone

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