Variant report

Variant	rs4643791
Chromosome Location	chr4:120265619-120265620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10003742	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10004114	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10015883	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10518300	0.82[CHD][hapmap]
rs10518329	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs1052633	0.80[CHD][hapmap]
rs11098498	0.80[CHD][hapmap]
rs11098506	0.87[CHB][hapmap]
rs1155577	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap]
rs11723550	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11724758	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11731571	0.82[CHD][hapmap]
rs11732621	0.80[CHD][hapmap]
rs12711071	0.82[CHD][hapmap]
rs13104219	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs13134517	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13139045	0.90[CHD][hapmap]
rs1480933	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs1511025	0.82[CHD][hapmap]
rs1546505	0.80[CHD][hapmap]
rs1814815	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980025	0.82[CHD][hapmap]
rs2017058	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2036858	0.83[AFR][1000 genomes]
rs28439855	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28551750	0.80[ASN][1000 genomes]
rs28691602	0.81[ASN][1000 genomes]
rs6815291	0.81[ASN][1000 genomes]
rs6824111	0.87[CHB][hapmap]
rs6843229	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs6843509	0.80[CHD][hapmap]
rs6844263	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7665125	0.83[CHB][hapmap]
rs7672594	0.82[CHD][hapmap]
rs878372	0.82[CHD][hapmap]
rs9637624	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9991959	0.82[CHD][hapmap]
rs9995136	0.87[CHB][hapmap]
rs9999724	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4643791	BBS7	cis	cerebellum	SCAN
rs4643791	USP53	cis	parietal	SCAN
rs4643791	TRPC3	cis	parietal	SCAN
rs4643791	SYNPO2	cis	cerebellum	SCAN
rs4643791	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs4643791	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120264400-120266400	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links