Variant report

Variant	rs17624756
Chromosome Location	chr5:147158403-147158404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10477342	0.91[EUR][1000 genomes]
rs12653862	0.84[EUR][1000 genomes]
rs12659905	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17497858	0.91[EUR][1000 genomes]
rs17497914	0.88[EUR][1000 genomes]
rs17498180	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17563332	0.84[EUR][1000 genomes]
rs17563872	0.92[EUR][1000 genomes]
rs17703007	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116770	0.91[EUR][1000 genomes]
rs28469761	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32204	0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4593256	0.91[EUR][1000 genomes]
rs4705042	0.91[EUR][1000 genomes]
rs6873548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895952	0.87[EUR][1000 genomes]
rs7735973	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686888	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	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
rs17624756	JAKMIP2	cis	Artery Tibial	GTEx
rs17624756	SH3RF2	cis	parietal	SCAN
rs17624756	MRPL45	trans	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147146800-147160600	Weak transcription	Primary T cells from cord blood	blood
2	chr5:147151200-147159400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr5:147151400-147160600	Weak transcription	Fetal Lung	lung
4	chr5:147153000-147159800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:147154600-147158600	Weak transcription	Brain Anterior Caudate	brain
6	chr5:147154600-147159200	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:147155600-147159600	Weak transcription	Fetal Thymus	thymus
8	chr5:147156000-147161400	Weak transcription	Primary B cells from cord blood	blood
9	chr5:147156200-147159400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:147156200-147161200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:147156400-147159400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:147156400-147159400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:147156600-147159800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:147156800-147158600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:147156800-147159400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:147157600-147159400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr5:147157600-147159400	Enhancers	Fetal Brain Male	brain
18	chr5:147157600-147159400	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:147157800-147158600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:147158000-147159400	Enhancers	Brain Germinal Matrix	brain
21	chr5:147158200-147158600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:147158200-147159600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr5:147158200-147160400	Enhancers	Brain Substantia Nigra	brain
24	chr5:147158400-147158600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:147158400-147158600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:147158400-147158800	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr5:147158400-147159200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr5:147158400-147159200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr5:147158400-147159400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:147158400-147159600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr5:147158400-147159600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links