Variant report

Variant	rs759890
Chromosome Location	chr12:29829723-29829724
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10128913	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10743668	0.80[AMR][1000 genomes]
rs10743669	0.81[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771560	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771561	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771563	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771564	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771566	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771567	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843475	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843489	0.82[CHB][hapmap]
rs11050352	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050353	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050354	0.94[YRI][hapmap]
rs12228730	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12229802	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2003607	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2033027	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033028	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033029	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033031	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033032	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033033	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033035	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033036	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033037	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2033040	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4617668	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298533	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759887	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs759888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7964894	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965351	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965504	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7965682	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29794400-29831800	Weak transcription	Ovary	ovary
2	chr12:29816600-29840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:29820200-29851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:29820400-29844200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:29821400-29829800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:29822400-29840200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:29825400-29833200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:29825400-29847800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:29825800-29832800	Weak transcription	Small Intestine	intestine
10	chr12:29826000-29829800	Weak transcription	Fetal Heart	heart
11	chr12:29827000-29830600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:29827600-29830200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr12:29828600-29830000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:29828600-29854000	Weak transcription	Aorta	Aorta
15	chr12:29829200-29829800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:29829200-29830000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:29829200-29830200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr12:29829200-29830400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:29829400-29829800	Enhancers	Right Atrium	heart
20	chr12:29829400-29829800	Enhancers	Spleen	Spleen
21	chr12:29829400-29830000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:29829400-29830000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:29829400-29830000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:29829400-29830000	Enhancers	Psoas Muscle	Psoas
25	chr12:29829400-29830000	Enhancers	Hela-S3	cervix
26	chr12:29829400-29830000	Enhancers	HSMMtube	muscle
27	chr12:29829400-29830200	Enhancers	Left Ventricle	heart
28	chr12:29829400-29830200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr12:29829400-29830200	Enhancers	HMEC	breast
30	chr12:29829400-29830200	Genic enhancers	HSMM	muscle
31	chr12:29829400-29830200	Enhancers	Osteobl	bone
32	chr12:29829400-29830600	Enhancers	Stomach Smooth Muscle	stomach
33	chr12:29829600-29829800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr12:29829600-29830000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr12:29829600-29830000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:29829600-29830000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:29829600-29830000	Enhancers	Fetal Muscle Leg	muscle

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