Variant report

Variant	rs534348
Chromosome Location	chr7:140782235-140782236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11762357	0.93[ASN][1000 genomes]
rs1860752	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2365575	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4726263	1.00[ASN][1000 genomes]
rs491554	1.00[ASN][1000 genomes]
rs498933	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs511001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536809	0.98[ASN][1000 genomes]
rs553046	1.00[ASN][1000 genomes]
rs55949610	0.94[ASN][1000 genomes]
rs560981	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6464278	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs6464330	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6944492	1.00[ASN][1000 genomes]
rs6960603	0.96[ASN][1000 genomes]
rs6962233	0.82[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[YRI][hapmap];0.94[ASN][1000 genomes]
rs6967482	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs722219	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7778658	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7805034	0.94[ASN][1000 genomes]
rs7806026	0.88[ASW][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7810146	0.89[ASN][1000 genomes]
rs801157	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801158	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9640323	0.94[ASN][1000 genomes]
rs9886312	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889248	chr7:140754785-140809205	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3417140	chr7:140768130-140783190	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs534348	NDUFB2	cis	lymphoblastoid	seeQTL
rs534348	TRPV5	cis	parietal	SCAN
rs534348	ADCK2	cis	cerebellum	SCAN
rs534348	OR6B1	cis	parietal	SCAN
rs534348	BRAF	Cis_1M	lymphoblastoid	RTeQTL
rs534348	MRPS33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140774800-140783200	Weak transcription	Pancreas	Pancrea
2	chr7:140776800-140782800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:140776800-140783200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:140776800-140783200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:140776800-140783200	Weak transcription	Brain Angular Gyrus	brain
6	chr7:140776800-140783200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:140776800-140783200	Weak transcription	Fetal Brain Male	brain
8	chr7:140777000-140785000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:140778000-140793200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:140778800-140783200	Weak transcription	Psoas Muscle	Psoas
11	chr7:140778800-140794400	Weak transcription	Fetal Brain Female	brain
12	chr7:140780200-140783200	Weak transcription	Gastric	stomach
13	chr7:140781800-140782400	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr7:140782000-140782600	Enhancers	Brain Germinal Matrix	brain
15	chr7:140782200-140783200	Weak transcription	Brain Inferior Temporal Lobe	brain

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