Variant report

Variant	rs13165524
Chromosome Location	chr5:146616381-146616382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10058805	0.83[EUR][1000 genomes]
rs10059785	0.82[EUR][1000 genomes]
rs10059845	0.83[EUR][1000 genomes]
rs10060001	0.81[EUR][1000 genomes]
rs10077015	0.83[EUR][1000 genomes]
rs11741699	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11742389	0.83[EUR][1000 genomes]
rs11750287	0.83[EUR][1000 genomes]
rs12186725	0.83[EUR][1000 genomes]
rs12187523	0.82[EUR][1000 genomes]
rs12187544	0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs13190267	0.84[EUR][1000 genomes]
rs1432649	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17106345	0.83[EUR][1000 genomes]
rs1835908	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs1835909	0.83[EUR][1000 genomes]
rs2400288	0.83[EUR][1000 genomes]
rs2400289	0.85[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2400290	0.82[EUR][1000 genomes]
rs2895678	0.82[EUR][1000 genomes]
rs2895679	0.82[EUR][1000 genomes]
rs34008203	0.82[EUR][1000 genomes]
rs34013186	0.82[EUR][1000 genomes]
rs34047526	0.82[EUR][1000 genomes]
rs34064519	0.86[EUR][1000 genomes]
rs34390085	0.82[EUR][1000 genomes]
rs34584308	0.83[EUR][1000 genomes]
rs35011974	0.82[EUR][1000 genomes]
rs35206295	0.82[EUR][1000 genomes]
rs35294904	0.84[EUR][1000 genomes]
rs35416734	0.82[EUR][1000 genomes]
rs35469676	0.82[EUR][1000 genomes]
rs35610443	0.82[EUR][1000 genomes]
rs36088388	0.81[EUR][1000 genomes]
rs4535507	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4546437	0.82[EUR][1000 genomes]
rs4705032	0.81[EUR][1000 genomes]
rs4705033	0.81[EUR][1000 genomes]
rs4705034	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4705035	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4705143	0.84[CEU][hapmap]
rs4705145	0.81[EUR][1000 genomes]
rs4705146	0.82[EUR][1000 genomes]
rs4705148	0.83[EUR][1000 genomes]
rs4705149	0.83[EUR][1000 genomes]
rs4705151	0.84[JPT][hapmap]
rs4705152	0.83[EUR][1000 genomes]
rs4705153	0.83[EUR][1000 genomes]
rs66508382	0.82[EUR][1000 genomes]
rs6868694	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs6870188	0.82[EUR][1000 genomes]
rs6870193	0.82[EUR][1000 genomes]
rs6870527	0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6871193	0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6871364	0.82[EUR][1000 genomes]
rs6886891	0.83[EUR][1000 genomes]
rs6890448	0.85[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs6891682	0.83[EUR][1000 genomes]
rs6891890	0.83[EUR][1000 genomes]
rs6895610	0.83[EUR][1000 genomes]
rs6898321	0.83[EUR][1000 genomes]
rs7701791	0.95[CEU][hapmap];0.86[EUR][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13165524	ZNF576	trans	parietal	SCAN
rs13165524	PLAC8L1	cis	cerebellum	SCAN
rs13165524	PDE6A	cis	parietal	SCAN
rs13165524	JAKMIP2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146614400-146617800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:146614800-146617800	Weak transcription	Gastric	stomach
3	chr5:146615000-146617800	Weak transcription	Pancreas	Pancrea
4	chr5:146615000-146618400	Weak transcription	Esophagus	oesophagus
5	chr5:146615000-146620800	Weak transcription	Psoas Muscle	Psoas
6	chr5:146615000-146621600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:146615200-146621400	Weak transcription	Aorta	Aorta
8	chr5:146615800-146616400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:146615800-146616400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr5:146615800-146616400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
11	chr5:146616000-146616400	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr5:146616200-146616400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:146616200-146616400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:146616200-146619400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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