Variant report

Variant	rs716389
Chromosome Location	chr17:15399737-15399738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:15398558..15401467-chr17:15404011..15406504,2	K562	blood:
2	chr17:15164136..15167626-chr17:15397793..15400943,4	K562	blood:
3	chr17:15392637..15397367-chr17:15398758..15404412,8	K562	blood:
4	chr17:15398558..15401467-chr17:15403715..15406504,4	K562	blood:
5	chr17:15392701..15397152-chr17:15398701..15402500,5	K562	blood:

Variant related genes	Relation type
ENSG00000109099	Chromatin interaction
ENSG00000265445	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11651787	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11653403	0.96[CEU][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs1465251	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs1465252	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2052022	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236810	0.85[LWK][hapmap];0.93[MKK][hapmap]
rs28411195	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28733269	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2938158	0.83[LWK][hapmap];0.92[MKK][hapmap]
rs3865257	0.82[EUR][1000 genomes]
rs4572441	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55749051	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62069953	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62072569	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62072571	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62072578	0.85[EUR][1000 genomes]
rs7211982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7215138	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8076852	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9899922	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9901383	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903674	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9904986	0.82[CHB][hapmap]
rs9908651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9911005	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9911822	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9913509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs716389	CDRT4	cis	cerebellum	SCAN
rs716389	TEKT3	cis	parietal	SCAN
rs716389	TEKT3	cis	cerebellum	SCAN
rs716389	CDRT4	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15359200-15404600	Weak transcription	Primary T cells from cord blood	blood
2	chr17:15368400-15405400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr17:15369000-15401600	Weak transcription	Brain Germinal Matrix	brain
4	chr17:15369200-15405000	Weak transcription	Esophagus	oesophagus
5	chr17:15377400-15406400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
7	chr17:15383400-15402200	Weak transcription	A549	lung
8	chr17:15383400-15455000	Weak transcription	Gastric	stomach
9	chr17:15383800-15401400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:15383800-15405200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr17:15383800-15406000	Weak transcription	NHEK	skin
12	chr17:15384600-15406200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
14	chr17:15387200-15400000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:15387200-15403800	Weak transcription	Liver	Liver
16	chr17:15387200-15417000	Weak transcription	Small Intestine	intestine
17	chr17:15387400-15405000	Weak transcription	Lung	lung
18	chr17:15388000-15401600	Weak transcription	Ovary	ovary
19	chr17:15388600-15406000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr17:15393000-15406000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:15393600-15399800	Enhancers	Brain Substantia Nigra	brain
23	chr17:15393600-15400400	Enhancers	Brain Hippocampus Middle	brain
24	chr17:15393800-15405400	Weak transcription	Colonic Mucosa	Colon
25	chr17:15394000-15400600	Enhancers	Brain Cingulate Gyrus	brain
26	chr17:15394400-15405800	Weak transcription	Aorta	Aorta
27	chr17:15394400-15406000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:15394600-15400600	Weak transcription	Fetal Heart	heart
29	chr17:15394600-15405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:15394600-15405000	Weak transcription	Fetal Lung	lung
31	chr17:15394600-15405000	Weak transcription	Spleen	Spleen
32	chr17:15394600-15405200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:15394600-15405200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr17:15394600-15405600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr17:15394600-15406400	Weak transcription	Stomach Mucosa	stomach
36	chr17:15394600-15417000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr17:15394800-15400200	Weak transcription	Fetal Brain Female	brain
38	chr17:15394800-15404800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr17:15394800-15405000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr17:15395000-15401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:15395000-15404800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:15395000-15405400	Weak transcription	NHLF	lung
44	chr17:15395000-15405600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr17:15395000-15410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:15395200-15403600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr17:15395400-15403800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr17:15395400-15405200	Weak transcription	Brain Angular Gyrus	brain
49	chr17:15395400-15413400	Weak transcription	Hela-S3	cervix
50	chr17:15395600-15400000	Weak transcription	NH-A	brain

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