Variant report

Variant	rs1465251
Chromosome Location	chr17:15407763-15407764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:15405279-15408288	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000223878	TF binding region
CDRT4	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11649792	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11651787	0.90[EUR][1000 genomes]
rs11653403	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1465252	0.90[EUR][1000 genomes]
rs1988028	0.81[EUR][1000 genomes]
rs2052022	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28411195	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28733269	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3865257	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4365325	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4572441	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55749051	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56407841	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62069953	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62072569	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072571	0.90[EUR][1000 genomes]
rs62072578	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62072579	0.80[EUR][1000 genomes]
rs716389	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs7211982	0.87[EUR][1000 genomes]
rs7215138	0.81[JPT][hapmap]
rs8076852	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9899922	0.83[EUR][1000 genomes]
rs9901383	0.87[EUR][1000 genomes]
rs9903674	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9906036	0.83[EUR][1000 genomes]
rs9908651	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9911005	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9911822	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9913509	0.96[CEU][hapmap];0.83[JPT][hapmap];0.90[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1465251	AC005517.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
2	chr17:15383400-15455000	Weak transcription	Gastric	stomach
3	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
4	chr17:15387200-15417000	Weak transcription	Small Intestine	intestine
5	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:15394600-15417000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:15395000-15410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:15395400-15413400	Weak transcription	Hela-S3	cervix
10	chr17:15396000-15417200	Weak transcription	Fetal Brain Male	brain
11	chr17:15396800-15420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:15398800-15408800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr17:15399000-15408800	Strong transcription	HepG2	liver
14	chr17:15400800-15413000	Weak transcription	NH-A	brain
15	chr17:15401200-15420400	Weak transcription	Psoas Muscle	Psoas
16	chr17:15402800-15410200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:15403000-15410200	Weak transcription	Fetal Brain Female	brain
18	chr17:15405400-15410200	Weak transcription	Primary T cells from cord blood	blood
19	chr17:15405400-15418200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr17:15405400-15419000	Weak transcription	Liver	Liver
21	chr17:15405600-15410200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:15405600-15411200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:15406000-15407800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:15406000-15410200	Weak transcription	Fetal Intestine Large	intestine
25	chr17:15406000-15411600	Weak transcription	Lung	lung
26	chr17:15406000-15411800	Weak transcription	HSMMtube	muscle
27	chr17:15406000-15416800	Weak transcription	K562	blood
28	chr17:15406200-15409000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:15406200-15411400	Weak transcription	Ovary	ovary
30	chr17:15406200-15414600	Weak transcription	Brain Angular Gyrus	brain
31	chr17:15406200-15414800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:15406200-15416800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:15406200-15420600	Weak transcription	Colonic Mucosa	Colon
34	chr17:15406600-15408000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:15406600-15408000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:15406600-15408400	Weak transcription	Fetal Intestine Small	intestine
37	chr17:15406600-15410000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr17:15406600-15410000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr17:15406600-15410200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr17:15406600-15410200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr17:15406600-15410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:15406600-15410200	Weak transcription	Brain Germinal Matrix	brain
43	chr17:15406600-15410400	Weak transcription	Fetal Heart	heart
44	chr17:15406600-15411400	Weak transcription	Fetal Muscle Leg	muscle
45	chr17:15406600-15411400	Weak transcription	Left Ventricle	heart
46	chr17:15406600-15411400	Weak transcription	NHDF-Ad	bronchial
47	chr17:15406600-15411400	Weak transcription	NHLF	lung
48	chr17:15406600-15411600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr17:15406600-15411800	Weak transcription	Right Atrium	heart
50	chr17:15406600-15412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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