Variant report

Variant	rs10400541
Chromosome Location	chr12:29720295-29720296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10400534	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	0.91[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs10771545	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs10771546	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs10771547	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs10771549	0.85[ASN][1000 genomes]
rs10771550	0.96[CEU][hapmap];0.83[JPT][hapmap];0.97[EUR][1000 genomes]
rs10771551	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10771552	0.94[EUR][1000 genomes]
rs10843443	0.84[ASN][1000 genomes]
rs10843445	0.95[EUR][1000 genomes]
rs10843446	0.92[ASN][1000 genomes]
rs11050270	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs11050271	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs11050273	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11050278	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs11050280	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs11050281	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs11050284	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050285	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11050288	0.94[ASN][1000 genomes]
rs11050291	0.94[ASN][1000 genomes]
rs11050292	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11050293	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs11050295	0.94[ASN][1000 genomes]
rs11050296	0.94[ASN][1000 genomes]
rs11050297	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11050298	0.88[ASN][1000 genomes]
rs11050299	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11050300	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11050301	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11050302	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11050308	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs11611194	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs12371221	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs12579805	0.86[CHB][hapmap]
rs12581671	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs12810291	0.94[ASN][1000 genomes]
rs12819780	0.82[CHB][hapmap]
rs12820673	0.86[ASN][1000 genomes]
rs1326758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1409616	0.86[CHB][hapmap]
rs148898	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1529908	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159685	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159687	0.95[EUR][1000 genomes]
rs159689	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs159690	0.96[EUR][1000 genomes]
rs159694	0.91[EUR][1000 genomes]
rs159695	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs159696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159697	0.95[EUR][1000 genomes]
rs159698	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs159701	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs159703	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs159704	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs159705	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs159707	0.91[CHB][hapmap]
rs159708	0.91[CHB][hapmap]
rs159709	0.82[CHB][hapmap]
rs159713	0.80[JPT][hapmap]
rs159714	0.86[CHB][hapmap]
rs177254	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs1988548	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2060569	0.85[ASN][1000 genomes]
rs2081429	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs2162033	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2194819	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs2209661	0.80[JPT][hapmap]
rs2243623	0.82[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2254945	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs2288131	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288132	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2288133	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2553077	0.86[CHB][hapmap]
rs2710775	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2766599	0.82[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2766600	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2766601	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2766602	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2766604	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs2766605	0.86[CHB][hapmap]
rs2766606	0.86[CHB][hapmap]
rs299444	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs299445	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs299453	0.89[EUR][1000 genomes]
rs299454	0.95[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs299455	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs299456	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs299457	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs299459	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs299467	0.95[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs299468	0.90[EUR][1000 genomes]
rs299470	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs299471	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs299479	0.95[CEU][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs299487	0.95[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs34020170	0.92[ASN][1000 genomes]
rs34187264	0.92[ASN][1000 genomes]
rs34555972	0.91[ASN][1000 genomes]
rs35111056	0.84[ASN][1000 genomes]
rs35536095	0.92[ASN][1000 genomes]
rs35741143	0.83[ASN][1000 genomes]
rs366998	0.89[EUR][1000 genomes]
rs375109	0.85[ASN][1000 genomes]
rs3910440	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3910441	0.82[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4931201	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs4931204	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57231427	0.96[EUR][1000 genomes]
rs60500145	0.92[ASN][1000 genomes]
rs6487837	0.81[ASN][1000 genomes]
rs7294502	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7295284	0.86[CHB][hapmap]
rs7301491	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7306397	0.85[ASN][1000 genomes]
rs7310555	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs7310895	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs7311193	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs7314549	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs7959535	0.80[JPT][hapmap]
rs7965227	0.80[JPT][hapmap]
rs7971202	0.85[ASN][1000 genomes]
rs9300191	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs9300192	0.81[ASN][1000 genomes]
rs9738399	0.90[ASN][1000 genomes]
rs994172	0.86[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: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	chr12:29700400-29734000	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	chr12:29717000-29721800	Weak transcription	HUVEC	blood vessel
20	chr12:29717400-29720400	Weak transcription	Fetal Heart	heart
21	chr12:29717400-29722200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:29717600-29721600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:29717600-29721600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:29717600-29725000	Weak transcription	Aorta	Aorta
25	chr12:29717600-29727400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:29717600-29727800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:29717600-29734800	Weak transcription	NHLF	lung
28	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
29	chr12:29717800-29721600	Weak transcription	HSMMtube	muscle
30	chr12:29717800-29732200	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:29718200-29725400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:29718600-29727600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:29718800-29723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:29719200-29721800	Weak transcription	HSMM	muscle
35	chr12:29719400-29721400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:29719400-29722800	Enhancers	Fetal Kidney	kidney
37	chr12:29719400-29724000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:29719600-29720600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:29719600-29721800	Weak transcription	NH-A	brain
40	chr12:29719600-29722200	Weak transcription	Fetal Stomach	stomach
41	chr12:29719600-29724600	Weak transcription	Right Ventricle	heart
42	chr12:29719600-29724600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:29719800-29721200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:29719800-29722200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:29719800-29724800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:29720000-29720400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:29720000-29720600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr12:29720000-29720800	Strong transcription	Hela-S3	cervix
49	chr12:29720000-29724200	Weak transcription	Left Ventricle	heart
50	chr12:29720000-29731400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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