Variant report

Variant	rs17053472
Chromosome Location	chr3:53788732-53788733
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17053453	0.94[CHD][hapmap];0.86[JPT][hapmap]
rs3774560	0.94[CHD][hapmap];0.86[JPT][hapmap]
rs3774580	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17053472	PDE12	cis	parietal	SCAN
rs17053472	ACTR8	cis	parietal	SCAN
rs17053472	RPL29	cis	parietal	SCAN
rs17053472	NPRL2	cis	parietal	SCAN
rs17053472	RBM5	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
2	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
4	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
5	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:53778800-53797000	Weak transcription	Pancreas	Pancrea
7	chr3:53779000-53806400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:53779800-53788800	Strong transcription	Brain Inferior Temporal Lobe	brain
9	chr3:53780400-53807000	Weak transcription	Fetal Brain Female	brain
10	chr3:53781800-53807400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:53783800-53790000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:53785000-53811200	Weak transcription	Spleen	Spleen
13	chr3:53785400-53795400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:53785800-53806600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:53786000-53795600	Weak transcription	Brain Angular Gyrus	brain
16	chr3:53786000-53808200	Weak transcription	Liver	Liver
17	chr3:53786800-53788800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr3:53787000-53790000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:53787200-53788800	Enhancers	Fetal Thymus	thymus
20	chr3:53787200-53788800	Enhancers	Dnd41	blood
21	chr3:53787200-53789200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:53787200-53789600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:53787400-53788800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:53787400-53788800	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:53787400-53788800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:53787400-53788800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:53787400-53788800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr3:53787400-53789000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:53787600-53788800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:53787800-53792800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:53788000-53788800	Enhancers	Lung	lung
32	chr3:53788200-53788800	Enhancers	GM12878-XiMat	blood
33	chr3:53788200-53789000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:53788200-53797400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:53788400-53788800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:53788600-53788800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:53788600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:53788600-53789400	Strong transcription	Fetal Kidney	kidney
39	chr3:53788600-53795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links