Variant report

Variant	rs17523562
Chromosome Location	chr5:15677834-15677835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10520820	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]
rs11748066	0.95[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11953541	0.93[YRI][hapmap]
rs11956557	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs13165753	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13165774	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13176043	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13177182	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13177283	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13184983	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13190262	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1429030	0.90[CEU][hapmap]
rs17523444	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17523486	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2059900	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs35283404	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35336928	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35839071	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4129028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4440359	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4509017	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4587075	0.90[CEU][hapmap];0.90[TSI][hapmap]
rs58149311	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60776566	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6554891	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6860057	0.90[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6864426	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6865410	0.91[CEU][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6871889	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]
rs6872217	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]
rs6878966	0.95[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6896719	1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes]
rs6897885	0.86[MEX][hapmap]
rs71595943	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7706195	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv597263	chr5:15672137-15720478	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv461983	chr5:15674635-15720106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv597264	chr5:15674635-15720106	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15665200-15680800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:15668400-15679000	Weak transcription	Brain Anterior Caudate	brain
3	chr5:15670400-15683200	Weak transcription	HUVEC	blood vessel
4	chr5:15672200-15684400	Weak transcription	NHDF-Ad	bronchial
5	chr5:15674200-15680000	Enhancers	Fetal Lung	lung
6	chr5:15674400-15684200	Weak transcription	HSMMtube	muscle
7	chr5:15675000-15680400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:15675200-15679400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:15675200-15687000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:15675200-15693000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:15675600-15678200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:15675800-15679400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:15675800-15679400	Weak transcription	Brain Substantia Nigra	brain
14	chr5:15675800-15686200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:15676000-15686000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:15676000-15687200	Weak transcription	Brain Angular Gyrus	brain
17	chr5:15676200-15680000	Enhancers	Fetal Stomach	stomach
18	chr5:15676200-15682200	Weak transcription	Aorta	Aorta
19	chr5:15676600-15680000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:15677000-15678200	Weak transcription	Fetal Heart	heart
21	chr5:15677000-15679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:15677000-15682200	Weak transcription	Left Ventricle	heart
23	chr5:15677000-15682800	Weak transcription	Fetal Kidney	kidney
24	chr5:15677000-15690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:15677200-15678000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:15677200-15682800	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:15677600-15683400	Weak transcription	Ovary	ovary

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