Variant report

Variant	rs17824137
Chromosome Location	chr14:63644114-63644115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17100818	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100827	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100839	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100842	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100844	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100849	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100865	0.82[GIH][hapmap]
rs17224223	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17824107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1957782	0.96[EUR][1000 genomes]
rs2223947	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56259683	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56265501	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58209565	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59442023	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59772452	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7142041	0.91[GIH][hapmap]
rs72712519	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712531	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72712532	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72712533	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72712537	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72712539	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72712540	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72712541	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72712542	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72712544	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712545	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8017562	0.88[EUR][1000 genomes]
rs9788522	0.91[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527251	chr14:63400786-64068806	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv520528	chr14:63400786-64157117	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv564893	chr14:63526931-63796122	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1045599	chr14:63540073-63765152	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv530774	chr14:63591348-64029881	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv902017	chr14:63604188-63674832	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17824137	TIMM9	cis	cerebellum	SCAN
rs17824137	C14orf39	cis	cerebellum	SCAN
rs17824137	GPHB5	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:63639800-63645600	Weak transcription	Right Atrium	heart
2	chr14:63640200-63644800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr14:63642000-63644200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:63642000-63645400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr14:63642000-63645600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:63642000-63645600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr14:63642000-63645800	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:63642000-63646800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:63642200-63644200	Weak transcription	HMEC	breast
10	chr14:63642200-63644400	Weak transcription	NHEK	skin
11	chr14:63642600-63645400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:63642800-63644800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:63642800-63647000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr14:63643400-63645000	Weak transcription	NH-A	brain
15	chr14:63644000-63645600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:63644000-63647200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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