Variant report

Variant	rs11939568
Chromosome Location	chr4:102810162-102810163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10016018	0.85[EUR][1000 genomes]
rs1027013	0.81[ASN][1000 genomes]
rs11097760	0.85[EUR][1000 genomes]
rs11097761	0.85[EUR][1000 genomes]
rs11736568	0.85[EUR][1000 genomes]
rs11930376	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931658	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11932972	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933157	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934097	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940934	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11942437	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13101528	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103438	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108400	0.85[EUR][1000 genomes]
rs13116542	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13126550	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13142517	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434472	0.85[EUR][1000 genomes]
rs1352174	0.82[ASN][1000 genomes]
rs1363067	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1386173	0.83[ASN][1000 genomes]
rs1843680	0.81[ASN][1000 genomes]
rs2216546	0.85[EUR][1000 genomes]
rs2631244	0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2631249	0.85[ASN][1000 genomes]
rs28396651	0.85[EUR][1000 genomes]
rs2850375	0.82[ASN][1000 genomes]
rs2850383	0.81[ASN][1000 genomes]
rs2851328	0.83[ASN][1000 genomes]
rs2851329	0.85[ASN][1000 genomes]
rs2851333	0.85[ASN][1000 genomes]
rs2851336	0.83[ASN][1000 genomes]
rs28625045	0.84[EUR][1000 genomes]
rs34166099	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34208976	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34321727	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34814827	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35201947	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35476121	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35860418	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733197	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3974649	0.85[EUR][1000 genomes]
rs3974650	0.85[EUR][1000 genomes]
rs4295265	0.87[ASN][1000 genomes]
rs4345184	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463068	0.85[EUR][1000 genomes]
rs4572884	0.85[EUR][1000 genomes]
rs4639076	0.85[EUR][1000 genomes]
rs4698839	0.85[EUR][1000 genomes]
rs4698971	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698975	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698977	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698978	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698979	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60448423	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816787	0.85[EUR][1000 genomes]
rs6830565	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662572	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679882	0.85[EUR][1000 genomes]
rs901406	0.89[ASN][1000 genomes]
rs923206	0.89[ASN][1000 genomes]
rs9790475	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999440	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv999861	chr4:102576115-102930562	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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	5 gene(s)	inside rSNPs	diseases
3	esv2757945	chr4:102662699-103008940	Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759269	chr4:102662699-103008940	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised 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	6 gene(s)	inside rSNPs	diseases
5	nsv1011180	chr4:102685236-102985945	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537202	chr4:102685236-102985945	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2757074	chr4:102772861-102933949	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2752360	chr4:102790822-102888822	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11939568	BANK1	Cis_1M	lymphoblastoid	RTeQTL
rs11939568	NHEDC2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102801600-102811200	Strong transcription	Primary B cells from cord blood	blood
2	chr4:102809200-102813000	ZNF genes & repeats	Primary B cells from peripheral blood	blood

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