Variant report

Variant	rs58290227
Chromosome Location	chr12:29740438-29740439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10492311	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11829731	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11829994	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11834102	0.88[EUR][1000 genomes]
rs11834291	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11837554	0.83[EUR][1000 genomes]
rs12310251	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12424239	0.93[EUR][1000 genomes]
rs12816393	0.82[EUR][1000 genomes]
rs12826893	0.90[EUR][1000 genomes]
rs142565	0.83[EUR][1000 genomes]
rs148897	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs159684	0.89[EUR][1000 genomes]
rs159688	0.85[EUR][1000 genomes]
rs159691	0.85[EUR][1000 genomes]
rs159692	0.85[EUR][1000 genomes]
rs159693	0.87[EUR][1000 genomes]
rs16934448	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16934474	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16934556	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934569	0.83[EUR][1000 genomes]
rs16934597	0.83[EUR][1000 genomes]
rs1966531	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288228	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299474	0.85[EUR][1000 genomes]
rs299478	0.83[EUR][1000 genomes]
rs299480	0.83[EUR][1000 genomes]
rs299484	0.87[EUR][1000 genomes]
rs299485	0.83[EUR][1000 genomes]
rs34318689	0.93[EUR][1000 genomes]
rs55793838	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55970961	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56255721	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56367916	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56398900	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57072643	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57816450	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59519970	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59915017	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60743264	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66750226	0.84[EUR][1000 genomes]
rs67491988	0.83[EUR][1000 genomes]
rs7301943	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73069591	0.82[ASN][1000 genomes]
rs73069592	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73069593	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73069598	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071505	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071510	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071517	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071519	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071533	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071556	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73071582	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073417	0.85[EUR][1000 genomes]
rs73073419	0.85[EUR][1000 genomes]
rs7315541	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74078415	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:39 , 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	chr12:29735400-29745800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:29735800-29741000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:29735800-29742400	Weak transcription	NHDF-Ad	bronchial
12	chr12:29736000-29742400	Weak transcription	HSMMtube	muscle
13	chr12:29736000-29743400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:29736000-29744200	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:29736000-29744200	Weak transcription	Right Atrium	heart
16	chr12:29736000-29752200	Weak transcription	HSMM	muscle
17	chr12:29736800-29742400	Weak transcription	NHLF	lung
18	chr12:29736800-29762800	Weak transcription	Fetal Stomach	stomach
19	chr12:29737000-29742400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:29737000-29742400	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:29737000-29742400	Weak transcription	Lung	lung
22	chr12:29737000-29743200	Weak transcription	Fetal Heart	heart
23	chr12:29737000-29744200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:29737000-29748400	Weak transcription	Spleen	Spleen
25	chr12:29737200-29742000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:29737200-29742200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:29737200-29742200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:29737200-29742400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:29737200-29742800	Weak transcription	Left Ventricle	heart
30	chr12:29737200-29744000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:29737200-29744200	Weak transcription	Ovary	ovary
32	chr12:29737200-29744200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:29737200-29746800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:29737200-29748400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:29737200-29761800	Weak transcription	Right Ventricle	heart
36	chr12:29737200-29762400	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:29737200-29762800	Weak transcription	Psoas Muscle	Psoas
38	chr12:29740000-29742400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:29740200-29741000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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