Variant report

Variant	rs17498180
Chromosome Location	chr5:147131749-147131750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10477342	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11167996	0.82[EUR][1000 genomes]
rs12653862	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12659905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13172946	1.00[AFR][1000 genomes]
rs1549912	0.82[EUR][1000 genomes]
rs17495305	1.00[AFR][1000 genomes]
rs17496036	1.00[AFR][1000 genomes]
rs17496399	1.00[AFR][1000 genomes]
rs17496550	1.00[AFR][1000 genomes]
rs17497229	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17497858	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17497914	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17561784	1.00[AFR][1000 genomes]
rs17562343	1.00[AFR][1000 genomes]
rs17563332	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17563872	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17624756	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17703007	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2053050	1.00[AFR][1000 genomes]
rs2053052	1.00[AFR][1000 genomes]
rs2116770	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28469761	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35130412	1.00[AFR][1000 genomes]
rs35285805	1.00[AFR][1000 genomes]
rs4593256	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705042	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4705189	1.00[AFR][1000 genomes]
rs4705190	1.00[AFR][1000 genomes]
rs6873548	0.92[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6895952	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs71580441	1.00[AFR][1000 genomes]
rs72835149	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7735973	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9686888	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17498180	SH3RF2	cis	parietal	SCAN
rs17498180	JAKMIP2	cis	Artery Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147078600-147146000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:147117400-147155800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:147122800-147133200	Enhancers	Brain Angular Gyrus	brain
4	chr5:147126600-147132200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:147126600-147132400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:147126800-147133000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:147127000-147132000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:147127200-147132000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr5:147128000-147132200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:147128200-147132200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:147128200-147132400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr5:147128200-147133400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr5:147128200-147134200	Enhancers	Brain Anterior Caudate	brain
14	chr5:147129000-147132000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:147129000-147132600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:147129000-147134000	Enhancers	Brain Substantia Nigra	brain
17	chr5:147129000-147136000	Weak transcription	Thymus	Thymus
18	chr5:147129600-147132600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:147129600-147134600	Enhancers	Brain Hippocampus Middle	brain
20	chr5:147129800-147132800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr5:147130200-147132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:147130200-147132200	Enhancers	Colon Smooth Muscle	Colon
23	chr5:147130400-147132000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:147130400-147132000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:147130400-147132000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:147131000-147132200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:147131000-147132200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr5:147131000-147132200	Enhancers	Fetal Stomach	stomach
29	chr5:147131000-147132400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:147131000-147132600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr5:147131000-147132600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:147131000-147133600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:147131200-147132200	Enhancers	H9 Cell Line	embryonic stem cell
34	chr5:147131200-147132200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:147131200-147132200	Enhancers	Rectal Smooth Muscle	rectum
36	chr5:147131200-147132600	Enhancers	Fetal Lung	lung
37	chr5:147131200-147132800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:147131200-147133200	Enhancers	Fetal Brain Male	brain
39	chr5:147131400-147132200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:147131400-147132200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:147131400-147133000	Enhancers	Brain Cingulate Gyrus	brain
42	chr5:147131400-147135200	Weak transcription	Fetal Thymus	thymus
43	chr5:147131600-147132000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:147131600-147132200	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links