Variant report

Variant	rs299475
Chromosome Location	chr12:29705252-29705253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:29692484..29694062-chr12:29704393..29706971,2	K562	blood:
2	chr12:29704988..29706078-chr12:30286679..30287383,3	MCF-7	breast:
3	chr12:29705003..29705553-chr12:30288330..30288940,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10492312	0.95[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs10771545	0.81[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs10771546	0.87[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs10771547	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs10771549	0.87[EUR][1000 genomes]
rs10771550	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10771551	0.91[ASN][1000 genomes]
rs10771552	0.82[ASN][1000 genomes]
rs10843443	0.86[EUR][1000 genomes]
rs10843445	0.93[ASN][1000 genomes]
rs10843446	0.88[EUR][1000 genomes]
rs11050270	0.80[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs11050271	0.87[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs11050273	0.87[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs11050278	0.87[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs11050280	0.87[CEU][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs11050281	0.91[EUR][1000 genomes]
rs11050285	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs11050288	0.88[EUR][1000 genomes]
rs11050291	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11050292	0.85[CEU][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs11050293	0.87[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11050295	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs11050296	0.88[EUR][1000 genomes]
rs11050297	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs11050298	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11050299	0.86[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11050300	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs11050301	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs11050302	0.87[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11050308	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs11611194	0.86[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs12368037	0.85[JPT][hapmap]
rs12371221	0.87[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs12372765	0.87[CHB][hapmap]
rs12581671	0.87[CEU][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs12810291	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs12820673	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1409615	0.83[CHB][hapmap]
rs1409616	0.81[JPT][hapmap]
rs148898	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs1529908	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs159685	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs159687	0.91[ASN][1000 genomes]
rs159689	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs159690	0.91[ASN][1000 genomes]
rs159694	0.91[ASN][1000 genomes]
rs159695	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs159697	0.91[ASN][1000 genomes]
rs159698	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs159699	0.91[CHB][hapmap]
rs159700	0.86[CHB][hapmap]
rs159701	0.81[JPT][hapmap]
rs159703	0.81[JPT][hapmap]
rs159704	0.84[JPT][hapmap]
rs159705	0.81[JPT][hapmap]
rs159708	0.81[JPT][hapmap]
rs159709	0.84[JPT][hapmap]
rs159713	0.82[CHB][hapmap]
rs159714	0.85[JPT][hapmap]
rs159716	0.83[CHB][hapmap]
rs177254	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1988548	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs2060569	0.87[EUR][1000 genomes]
rs2081429	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2113879	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2113880	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162033	0.89[ASN][1000 genomes]
rs2194819	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs2209660	0.83[CHB][hapmap]
rs2209662	0.83[CHB][hapmap]
rs2225065	0.83[CHB][hapmap]
rs2243623	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs2254945	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs2288132	0.87[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs2288133	0.81[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs2288230	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2350532	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2553077	0.81[JPT][hapmap]
rs2710775	0.91[ASN][1000 genomes]
rs2766599	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs2766600	0.90[ASN][1000 genomes]
rs2766601	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs2766602	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs2766604	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2766605	0.84[JPT][hapmap]
rs2766606	0.81[JPT][hapmap]
rs299453	0.87[ASN][1000 genomes]
rs299454	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs299455	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs299458	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299459	0.87[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs299462	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299464	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299465	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299466	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299467	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299468	0.91[ASN][1000 genomes]
rs299470	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299471	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs299472	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299479	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs299487	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs34020170	0.85[EUR][1000 genomes]
rs34187264	0.85[EUR][1000 genomes]
rs34555972	0.91[EUR][1000 genomes]
rs35111056	0.84[EUR][1000 genomes]
rs35536095	0.88[EUR][1000 genomes]
rs35741143	0.84[EUR][1000 genomes]
rs366998	0.87[ASN][1000 genomes]
rs375109	0.88[EUR][1000 genomes]
rs3910440	0.91[CHB][hapmap]
rs3910441	0.90[CHB][hapmap]
rs4931201	0.87[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs57231427	0.91[ASN][1000 genomes]
rs60500145	0.88[EUR][1000 genomes]
rs6487837	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7294502	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs7301491	0.81[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs7306397	0.88[EUR][1000 genomes]
rs7310555	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs7310895	0.87[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs7311193	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7314549	0.81[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs7971202	0.88[EUR][1000 genomes]
rs9300191	0.81[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9300192	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9738399	0.86[EUR][1000 genomes]
rs994171	0.83[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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29668800-29706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:29673600-29708800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:29688200-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:29691000-29705800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:29691200-29709200	Weak transcription	HMEC	breast
8	chr12:29693000-29705600	Weak transcription	Hela-S3	cervix
9	chr12:29696400-29706000	Weak transcription	Aorta	Aorta
10	chr12:29696600-29705600	Weak transcription	Osteobl	bone
11	chr12:29698200-29712600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:29699400-29709600	Weak transcription	Left Ventricle	heart
13	chr12:29699400-29715800	Weak transcription	Right Ventricle	heart
14	chr12:29699800-29708800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:29700000-29712000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:29700200-29712200	Weak transcription	Ovary	ovary
17	chr12:29700400-29712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
20	chr12:29700600-29708800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:29700600-29711400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:29700800-29705800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:29700800-29707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:29700800-29709000	Weak transcription	HSMM	muscle
25	chr12:29700800-29709600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:29701000-29705600	Weak transcription	Liver	Liver
27	chr12:29701000-29705800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:29701000-29709400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:29701000-29714200	Weak transcription	HSMMtube	muscle
30	chr12:29701200-29705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:29701200-29705800	Weak transcription	Adipose Nuclei	Adipose
32	chr12:29701200-29714400	Weak transcription	NHDF-Ad	bronchial
33	chr12:29701200-29714400	Weak transcription	NHLF	lung
34	chr12:29701200-29715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:29701200-29715600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:29701400-29705800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:29701400-29711600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:29701600-29705400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:29701600-29706000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:29701600-29706000	Weak transcription	Gastric	stomach
41	chr12:29703800-29706000	Weak transcription	Psoas Muscle	Psoas
42	chr12:29703800-29715200	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:29704000-29709200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:29704800-29706200	Enhancers	Fetal Kidney	kidney
45	chr12:29705000-29711600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:29705000-29716000	Weak transcription	Spleen	Spleen

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