Variant report

Variant	rs12659905
Chromosome Location	chr5:147133740-147133741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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]
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]
rs17498180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12659905	SH3RF2	cis	parietal	SCAN
rs12659905	MRPL45	trans	parietal	SCAN
rs12659905	JAKMIP2	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 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	chr5:147128200-147134200	Enhancers	Brain Anterior Caudate	brain
4	chr5:147129000-147134000	Enhancers	Brain Substantia Nigra	brain
5	chr5:147129000-147136000	Weak transcription	Thymus	Thymus
6	chr5:147129600-147134600	Enhancers	Brain Hippocampus Middle	brain
7	chr5:147131400-147135200	Weak transcription	Fetal Thymus	thymus
8	chr5:147132000-147134200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr5:147132000-147138000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:147132200-147138400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:147132200-147139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:147132400-147139000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:147132600-147142000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:147132800-147146200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:147133000-147134600	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr5:147133000-147139000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:147133000-147143000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:147133200-147142000	Weak transcription	Brain Angular Gyrus	brain
19	chr5:147133200-147145600	Weak transcription	Fetal Brain Male	brain
20	chr5:147133400-147143000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:147133600-147146000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links