Variant report

Variant	rs55793838
Chromosome Location	chr12:29686971-29686972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10492311	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829731	0.91[AMR][1000 genomes]
rs11829994	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834102	0.80[EUR][1000 genomes]
rs11834291	0.91[AMR][1000 genomes]
rs12310251	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424239	0.85[EUR][1000 genomes]
rs12826893	0.80[EUR][1000 genomes]
rs148897	0.86[AMR][1000 genomes]
rs16934448	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934474	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16934556	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1966531	0.82[ASN][1000 genomes]
rs2288228	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs299474	0.83[EUR][1000 genomes]
rs34318689	0.85[EUR][1000 genomes]
rs55970961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56255721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56367916	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56398900	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57072643	0.82[ASN][1000 genomes]
rs57816450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58290227	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59519970	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59915017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743264	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66750226	0.82[ASN][1000 genomes]
rs7301943	0.91[AMR][1000 genomes]
rs73069591	1.00[ASN][1000 genomes]
rs73069592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069593	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069598	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071505	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071510	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071517	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071519	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071533	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071556	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071582	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73073417	0.82[ASN][1000 genomes]
rs73073419	0.82[ASN][1000 genomes]
rs7315541	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74078415	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29650400-29699000	Weak transcription	Right Ventricle	heart
2	chr12:29658400-29690200	Weak transcription	HMEC	breast
3	chr12:29660800-29690000	Weak transcription	NHDF-Ad	bronchial
4	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:29667200-29695600	Weak transcription	Ovary	ovary
6	chr12:29668600-29690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:29668600-29695800	Weak transcription	Aorta	Aorta
8	chr12:29668800-29706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:29670600-29687000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:29670600-29687800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:29670600-29697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:29670600-29699000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:29671000-29688000	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:29671000-29697200	Weak transcription	Spleen	Spleen
16	chr12:29671600-29695400	Weak transcription	Fetal Stomach	stomach
17	chr12:29671600-29697200	Weak transcription	Left Ventricle	heart
18	chr12:29673600-29708800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:29673800-29687600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:29675800-29689400	Weak transcription	Hela-S3	cervix
21	chr12:29678000-29690000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:29678400-29695000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:29680600-29690400	Weak transcription	Fetal Kidney	kidney
24	chr12:29681600-29690400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:29681600-29695600	Weak transcription	Adipose Nuclei	Adipose
26	chr12:29681600-29695800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:29682200-29697400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:29683600-29692800	Weak transcription	Psoas Muscle	Psoas
29	chr12:29686000-29687400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:29686000-29688000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:29686200-29690800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:29686400-29687800	Enhancers	HSMM	muscle
33	chr12:29686800-29687000	Genic enhancers	Muscle Satellite Cultured Cells	--
34	chr12:29686800-29687000	Enhancers	Gastric	stomach
35	chr12:29686800-29687200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
36	chr12:29686800-29687400	Enhancers	Brain Substantia Nigra	brain
37	chr12:29686800-29688200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:29686800-29688200	Enhancers	HSMMtube	muscle

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