Variant report

Variant	rs3020071
Chromosome Location	chr11:93105965-93105966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1004417	0.92[CEU][hapmap];0.98[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1456239	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1456242	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs1598546	0.85[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs1598547	0.89[EUR][1000 genomes]
rs1869913	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960665	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1975819	0.88[EUR][1000 genomes]
rs2124559	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2259469	0.98[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2259630	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2260769	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2605575	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2605576	0.96[CEU][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2605577	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2605578	0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2605579	0.98[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2658771	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2658774	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2925353	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2925359	0.89[EUR][1000 genomes]
rs2925363	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3019203	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019204	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019218	0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3019219	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs3019220	0.88[EUR][1000 genomes]
rs3019227	0.89[EUR][1000 genomes]
rs3019229	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3019230	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3020055	0.82[EUR][1000 genomes]
rs3020070	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020072	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3020075	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3020080	0.88[EUR][1000 genomes]
rs975916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv468793	chr11:93068163-93129893	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3020071	CCDC67	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93103800-93107600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:93105400-93106200	Enhancers	H9 Cell Line	embryonic stem cell
3	chr11:93105600-93106600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr11:93105600-93106600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr11:93105800-93106400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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