Variant report

Variant	rs11829994
Chromosome Location	chr12:29700793-29700794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10492311	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829731	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11834102	0.87[EUR][1000 genomes]
rs11834291	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11837554	0.82[JPT][hapmap]
rs12310251	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12811228	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12816393	0.81[CEU][hapmap]
rs12826893	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs142565	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs148897	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs159684	0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs16934448	0.83[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934474	0.88[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16934556	0.90[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1966531	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2288228	0.90[CEU][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs299474	0.89[EUR][1000 genomes]
rs299477	0.83[CEU][hapmap]
rs299478	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs299480	0.82[EUR][1000 genomes]
rs299484	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs299485	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs34318689	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs55793838	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55970961	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56255721	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56367916	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56398900	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57072643	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57816450	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58290227	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59519970	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59915017	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743264	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66750226	0.82[ASN][1000 genomes]
rs7301943	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73069591	1.00[ASN][1000 genomes]
rs73069592	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069593	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069598	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071505	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071510	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071517	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071519	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071533	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071556	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071582	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73073417	0.82[ASN][1000 genomes]
rs73073419	0.82[ASN][1000 genomes]
rs7315541	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078415	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv983497	chr12:29696128-29702801	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:49 , 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	chr12:29697200-29701400	Enhancers	Fetal Muscle Leg	muscle
12	chr12:29697400-29701400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:29698000-29701200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:29698000-29701400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:29698200-29712600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:29698600-29701200	Enhancers	NHDF-Ad	bronchial
17	chr12:29698800-29701200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:29698800-29701200	Enhancers	NHLF	lung
19	chr12:29699000-29700800	Enhancers	HSMM	muscle
20	chr12:29699200-29701000	Enhancers	HSMMtube	muscle
21	chr12:29699200-29701600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:29699400-29701000	Enhancers	Liver	Liver
23	chr12:29699400-29701200	Enhancers	Fetal Stomach	stomach
24	chr12:29699400-29704800	Weak transcription	Spleen	Spleen
25	chr12:29699400-29709600	Weak transcription	Left Ventricle	heart
26	chr12:29699400-29715800	Weak transcription	Right Ventricle	heart
27	chr12:29699600-29700800	Enhancers	Stomach Smooth Muscle	stomach
28	chr12:29699600-29701000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr12:29699800-29700800	Weak transcription	Lung	lung
30	chr12:29699800-29701000	Bivalent Enhancer	Fetal Lung	lung
31	chr12:29699800-29708800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:29700000-29700800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:29700000-29700800	Enhancers	NH-A	brain
34	chr12:29700000-29701000	Enhancers	Fetal Kidney	kidney
35	chr12:29700000-29701200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:29700000-29701200	Enhancers	Adipose Nuclei	Adipose
37	chr12:29700000-29712000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:29700200-29701000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:29700200-29701000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:29700200-29712200	Weak transcription	Ovary	ovary
41	chr12:29700400-29700800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:29700400-29701600	Enhancers	Psoas Muscle	Psoas
43	chr12:29700400-29712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
46	chr12:29700600-29700800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:29700600-29701000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:29700600-29708800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:29700600-29711400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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