Variant report

Variant	rs11653403
Chromosome Location	chr17:15421167-15421168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:74032040..74034358-chr17:15420239..15421739,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168209	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11649792	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11651787	0.91[EUR][1000 genomes]
rs1465251	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	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28411195	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28733269	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3865257	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4365325	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4572441	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55749051	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56407841	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62069953	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62072569	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62072571	0.91[EUR][1000 genomes]
rs62072578	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62072579	0.81[EUR][1000 genomes]
rs716389	0.96[CEU][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs7211982	0.88[EUR][1000 genomes]
rs7215138	0.81[JPT][hapmap]
rs8076852	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9899922	0.83[EUR][1000 genomes]
rs9901383	0.87[EUR][1000 genomes]
rs9903674	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9906036	0.83[EUR][1000 genomes]
rs9908651	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9911005	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9911822	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9913509	0.96[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]

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	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	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
5	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
6	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
7	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
rs11653403	AC005517.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383400-15455000	Weak transcription	Gastric	stomach
2	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:15406600-15422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:15406600-15428800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:15406800-15421800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:15406800-15422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:15406800-15450600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:15407000-15422400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr17:15410200-15426200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:15410800-15429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:15413800-15428000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr17:15414000-15429000	Weak transcription	Fetal Heart	heart
14	chr17:15414000-15430200	Weak transcription	Right Ventricle	heart
15	chr17:15414600-15422200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:15414600-15428000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr17:15415200-15422400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:15415200-15422600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:15415400-15422400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr17:15416200-15466000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:15416400-15421800	Strong transcription	Hela-S3	cervix
22	chr17:15417000-15422000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:15417000-15422200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr17:15417200-15421200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:15417400-15421600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:15417400-15422000	Strong transcription	Primary T cells from cord blood	blood
27	chr17:15417400-15422200	Weak transcription	Small Intestine	intestine
28	chr17:15417600-15427200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr17:15417600-15466400	Weak transcription	Ovary	ovary
30	chr17:15417800-15428200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:15418000-15429200	Weak transcription	Colon Smooth Muscle	Colon
32	chr17:15418200-15421800	Strong transcription	HSMMtube	muscle
33	chr17:15418200-15423000	Strong transcription	Fetal Stomach	stomach
34	chr17:15418400-15422400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr17:15418400-15422800	Strong transcription	Fetal Intestine Small	intestine
36	chr17:15418400-15430000	Weak transcription	K562	blood
37	chr17:15418400-15430200	Weak transcription	Pancreas	Pancrea
38	chr17:15418600-15429600	Weak transcription	Brain Substantia Nigra	brain
39	chr17:15418600-15450600	Weak transcription	Brain Angular Gyrus	brain
40	chr17:15418800-15422400	Strong transcription	HepG2	liver
41	chr17:15418800-15450600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:15419000-15422000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:15419000-15422400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:15419000-15422400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr17:15419200-15422400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:15419200-15422400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:15419400-15421200	Strong transcription	Aorta	Aorta
48	chr17:15419400-15421200	Strong transcription	Fetal Kidney	kidney
49	chr17:15419400-15421600	Weak transcription	Esophagus	oesophagus
50	chr17:15419600-15421200	ZNF genes & repeats	Osteobl	bone

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