Variant report

Variant	rs17547112
Chromosome Location	chr5:146689785-146689786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10875622	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12652074	0.85[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1582611	0.91[CHB][hapmap];0.82[GIH][hapmap];0.80[ASN][1000 genomes]
rs35267617	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6866338	0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17547112	SPINK1	cis	cerebellum	SCAN
rs17547112	TCOF1	cis	parietal	SCAN
rs17547112	RTN4	trans	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146684200-146689800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:146685000-146689800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:146687800-146690200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:146688600-146690200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:146688600-146690600	Enhancers	HUVEC	blood vessel
6	chr5:146688600-146691000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr5:146688800-146690000	Enhancers	NH-A	brain
8	chr5:146688800-146691200	Weak transcription	Lung	lung
9	chr5:146688800-146707200	Weak transcription	Pancreas	Pancrea
10	chr5:146689000-146690200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:146689000-146690200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr5:146689200-146690400	Enhancers	HSMM	muscle
13	chr5:146689200-146690800	Enhancers	Osteobl	bone
14	chr5:146689400-146690600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:146689600-146690000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:146689600-146690000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:146689600-146690000	Enhancers	Aorta	Aorta
18	chr5:146689600-146690000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr5:146689600-146690400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:146689600-146690400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:146689600-146690400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr5:146689600-146690400	Enhancers	Stomach Mucosa	stomach
23	chr5:146689600-146690400	Flanking Active TSS	A549	lung
24	chr5:146689600-146690400	Enhancers	HMEC	breast
25	chr5:146689600-146690400	Enhancers	HSMMtube	muscle
26	chr5:146689600-146690600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:146689600-146690600	Enhancers	Hela-S3	cervix
28	chr5:146689600-146691000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:146689600-146691000	Enhancers	Adipose Nuclei	Adipose
30	chr5:146689600-146691200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links