Variant report

Variant	rs1598546
Chromosome Location	chr11:93093373-93093374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004417	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10831029	0.87[CHB][hapmap]
rs10831032	0.81[CHB][hapmap]
rs12273033	0.82[CHB][hapmap]
rs12277063	0.87[CHB][hapmap]
rs12292127	0.81[CHB][hapmap]
rs12295955	0.81[CHB][hapmap]
rs1456239	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1456242	0.96[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1598547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869913	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1960665	0.89[EUR][1000 genomes]
rs1975819	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2124559	0.96[CEU][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2259469	0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2259630	0.86[EUR][1000 genomes]
rs2605575	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2605576	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2605577	0.84[EUR][1000 genomes]
rs2605578	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2605579	0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2658771	0.85[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2658774	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2925353	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2925359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2925363	0.84[EUR][1000 genomes]
rs3019203	0.89[EUR][1000 genomes]
rs3019204	0.89[EUR][1000 genomes]
rs3019218	0.88[CEU][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3019219	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3019220	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3019227	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019229	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3019230	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3020055	0.83[EUR][1000 genomes]
rs3020070	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3020071	0.85[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs3020072	0.85[EUR][1000 genomes]
rs3020075	0.85[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs3020080	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs975916	0.85[CEU][hapmap]
rs977255	0.82[CHB][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
rs1598546	CCDC67	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93090200-93094400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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