Variant report

Variant	rs2113879
Chromosome Location	chr12:29736480-29736481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10492312	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs10771545	0.83[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap]
rs10771546	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs10771547	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs10771549	0.82[EUR][1000 genomes]
rs10771550	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10771551	0.89[ASN][1000 genomes]
rs10771552	0.88[ASN][1000 genomes]
rs10843443	0.81[EUR][1000 genomes]
rs10843445	0.86[ASN][1000 genomes]
rs10843446	0.93[EUR][1000 genomes]
rs11050270	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs11050271	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs11050273	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap]
rs11050278	0.88[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs11050280	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11050281	0.89[EUR][1000 genomes]
rs11050285	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs11050288	0.92[EUR][1000 genomes]
rs11050291	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs11050292	0.87[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs11050293	0.88[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs11050295	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs11050296	0.92[EUR][1000 genomes]
rs11050297	0.88[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs11050298	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11050299	0.87[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs11050300	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs11050301	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs11050302	0.88[CEU][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes]
rs11050308	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs11611194	0.87[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs12368037	0.82[JPT][hapmap]
rs12371221	0.88[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs12372765	0.82[CHB][hapmap]
rs12581671	0.88[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs12810291	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs12820673	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1409615	0.87[CHB][hapmap]
rs1409616	0.83[JPT][hapmap]
rs148898	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs1529908	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs159685	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs159687	0.91[ASN][1000 genomes]
rs159689	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs159690	0.91[ASN][1000 genomes]
rs159694	0.90[ASN][1000 genomes]
rs159695	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[ASN][1000 genomes]
rs159697	0.91[ASN][1000 genomes]
rs159698	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs159699	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs159700	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs159701	0.83[JPT][hapmap]
rs159703	0.83[JPT][hapmap]
rs159704	0.83[JPT][hapmap]
rs159705	0.83[JPT][hapmap]
rs159708	0.83[JPT][hapmap]
rs159709	0.83[JPT][hapmap]
rs159713	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs159714	0.83[JPT][hapmap]
rs159716	0.87[CHB][hapmap]
rs177254	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1988548	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2060569	0.82[EUR][1000 genomes]
rs2081429	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2113880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162033	0.88[ASN][1000 genomes]
rs2194819	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[ASN][1000 genomes]
rs2209660	0.87[CHB][hapmap]
rs2209662	0.87[CHB][hapmap]
rs2225065	0.87[CHB][hapmap]
rs2243623	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2254945	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][1000 genomes]
rs2288132	0.88[CEU][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap]
rs2288133	0.83[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap]
rs2288230	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2350532	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553077	0.82[JPT][hapmap]
rs2710775	0.89[ASN][1000 genomes]
rs2766599	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2766600	0.89[ASN][1000 genomes]
rs2766601	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2766602	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs2766604	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2766605	0.83[JPT][hapmap]
rs2766606	0.83[JPT][hapmap]
rs299453	0.80[ASN][1000 genomes]
rs299454	0.95[CHB][hapmap];0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs299455	0.88[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs299458	0.83[ASN][1000 genomes]
rs299459	0.88[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs299462	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299463	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299464	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299465	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299466	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299467	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs299468	0.85[ASN][1000 genomes]
rs299470	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs299471	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs299472	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs299475	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]
rs299479	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs299487	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs34020170	0.88[EUR][1000 genomes]
rs34187264	0.88[EUR][1000 genomes]
rs34555972	0.89[EUR][1000 genomes]
rs35536095	0.93[EUR][1000 genomes]
rs366998	0.81[ASN][1000 genomes]
rs375109	0.83[EUR][1000 genomes]
rs3910440	0.86[CHB][hapmap]
rs3910441	0.86[CHB][hapmap]
rs4931201	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs57231427	0.89[ASN][1000 genomes]
rs60500145	0.92[EUR][1000 genomes]
rs6487837	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7294502	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7301491	0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs7306397	0.83[EUR][1000 genomes]
rs7310555	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7310895	0.88[CEU][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7311193	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7314549	0.83[CEU][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap]
rs7959535	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs7965227	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs7971202	0.83[EUR][1000 genomes]
rs9300191	0.83[CEU][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9300192	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9738399	0.91[EUR][1000 genomes]
rs994171	0.87[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	chr12:29709800-29756200	Weak transcription	HMEC	breast
2	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:29720200-29743600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:29729400-29744000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:29731000-29742600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
9	chr12:29732000-29737200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:29732200-29737200	Enhancers	Colon Smooth Muscle	Colon
11	chr12:29733600-29737000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:29733800-29737200	Enhancers	Adipose Nuclei	Adipose
13	chr12:29734000-29736600	Enhancers	Brain Anterior Caudate	brain
14	chr12:29734200-29737200	Enhancers	Rectal Smooth Muscle	rectum
15	chr12:29734600-29737000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:29734600-29737000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:29734600-29737200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:29734800-29736800	Enhancers	NHLF	lung
19	chr12:29734800-29737200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:29735200-29736600	Enhancers	Brain Cingulate Gyrus	brain
21	chr12:29735200-29737000	Enhancers	Spleen	Spleen
22	chr12:29735200-29737200	Enhancers	Left Ventricle	heart
23	chr12:29735400-29737000	Enhancers	Fetal Heart	heart
24	chr12:29735400-29737200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:29735400-29745800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:29735600-29736600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr12:29735600-29737200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr12:29735800-29741000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:29735800-29742400	Weak transcription	NHDF-Ad	bronchial
30	chr12:29736000-29736600	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:29736000-29737000	Weak transcription	Small Intestine	intestine
32	chr12:29736000-29742400	Weak transcription	HSMMtube	muscle
33	chr12:29736000-29743400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:29736000-29744200	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:29736000-29744200	Weak transcription	Right Atrium	heart
36	chr12:29736000-29752200	Weak transcription	HSMM	muscle
37	chr12:29736200-29736600	Weak transcription	Ovary	ovary
38	chr12:29736200-29736800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:29736200-29737000	Enhancers	Liver	Liver
40	chr12:29736200-29737200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:29736200-29737200	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr12:29736200-29737200	Enhancers	Right Ventricle	heart
43	chr12:29736400-29736800	Enhancers	Fetal Stomach	stomach
44	chr12:29736400-29737000	Enhancers	Lung	lung
45	chr12:29736400-29737200	Enhancers	Psoas Muscle	Psoas
46	chr12:29736400-29740200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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