Variant report

Variant	rs10520820
Chromosome Location	chr5:15635874-15635875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11748066	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11956557	0.86[CEU][hapmap]
rs12187518	0.83[YRI][hapmap]
rs13165753	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13165774	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13176043	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13176349	0.80[AFR][1000 genomes]
rs13177182	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13177283	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13184983	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13190262	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1429030	0.95[CEU][hapmap]
rs17523312	0.83[YRI][hapmap]
rs17523444	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17523486	0.86[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17523562	0.95[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2059900	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs35283404	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35336928	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35839071	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4129028	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4440359	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4509017	1.00[CEU][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4587075	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[LWK][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs58149311	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60776566	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6554891	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6860057	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6864426	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6865410	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6871889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[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]
rs6872217	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6878966	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6896719	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6897885	0.86[MEX][hapmap]
rs71595943	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7706195	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv4732	chr5:15598325-15636520	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15600600-15645400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:15627600-15648000	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:15627800-15637000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:15631400-15645200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:15633600-15644600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:15633800-15637000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:15634000-15638000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:15634600-15636000	Enhancers	HSMM	muscle
9	chr5:15634800-15636800	Enhancers	Fetal Heart	heart
10	chr5:15635000-15636000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:15635000-15636000	Enhancers	Brain Angular Gyrus	brain
12	chr5:15635000-15636000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr5:15635000-15636200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:15635200-15636000	Enhancers	Brain Anterior Caudate	brain
15	chr5:15635200-15636000	Enhancers	Esophagus	oesophagus
16	chr5:15635200-15636000	Genic enhancers	Fetal Stomach	stomach
17	chr5:15635200-15636000	Enhancers	Left Ventricle	heart
18	chr5:15635400-15637800	Enhancers	Brain Cingulate Gyrus	brain
19	chr5:15635600-15636600	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:15635600-15637200	Weak transcription	Psoas Muscle	Psoas
21	chr5:15635600-15641000	Weak transcription	Ovary	ovary
22	chr5:15635600-15642600	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:15635600-15643800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:15635600-15646800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:15635800-15636000	Flanking Active TSS	HSMMtube	muscle
26	chr5:15635800-15636400	Weak transcription	Osteobl	bone
27	chr5:15635800-15636800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:15635800-15637600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:15635800-15638200	Weak transcription	Right Atrium	heart
30	chr5:15635800-15640200	Weak transcription	Right Ventricle	heart
31	chr5:15635800-15643600	Weak transcription	Aorta	Aorta
32	chr5:15635800-15645000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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