Variant report

Variant	rs4802066
Chromosome Location	chr19:38109301-38109302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1038084	0.82[CEU][hapmap]
rs1038085	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10407657	0.82[CEU][hapmap]
rs10417204	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10424612	0.82[CEU][hapmap]
rs10425671	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11665877	0.84[EUR][1000 genomes]
rs11667454	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11667457	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668434	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs11668558	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs11670655	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11672077	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11883392	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1236810	0.90[CHB][hapmap];1.00[MKK][hapmap]
rs12972712	0.85[EUR][1000 genomes]
rs12981237	0.84[EUR][1000 genomes]
rs12982288	0.85[EUR][1000 genomes]
rs12983298	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1465434	0.90[CHB][hapmap]
rs17306508	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs17306795	1.00[CHB][hapmap]
rs1871197	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045909	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126978	0.82[CEU][hapmap]
rs2160640	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2199644	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291000	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385116	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385124	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385125	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs241940	0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap]
rs241941	0.90[CHB][hapmap]
rs241942	0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap]
rs241947	0.80[EUR][1000 genomes]
rs241948	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs241951	1.00[CHB][hapmap]
rs2617789	0.90[CHB][hapmap]
rs2927741	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2927744	0.82[CEU][hapmap]
rs2972453	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972454	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972456	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972459	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112435	0.85[EUR][1000 genomes]
rs34351186	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34607899	0.87[EUR][1000 genomes]
rs34782935	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35015599	0.85[EUR][1000 genomes]
rs35214625	0.85[EUR][1000 genomes]
rs35273320	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35415221	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36020184	0.84[EUR][1000 genomes]
rs36092052	0.84[EUR][1000 genomes]
rs3752365	0.94[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes]
rs4273159	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482404	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4802069	0.82[CEU][hapmap]
rs4803216	0.82[CEU][hapmap]
rs4803228	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803277	1.00[ASW][hapmap]
rs57308437	0.85[EUR][1000 genomes]
rs62108304	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108339	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62108355	0.85[EUR][1000 genomes]
rs6508729	0.90[CHB][hapmap];1.00[MKK][hapmap]
rs6508738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251097	0.82[CHB][hapmap]
rs7253174	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254828	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7255283	0.82[CEU][hapmap]
rs8111055	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8113076	0.82[CEU][hapmap]
rs856302	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]

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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4802066	RABAC1	cis	cerebellum	SCAN
rs4802066	ARHGEF1	cis	cerebellum	SCAN
rs4802066	CD3EAP	cis	cerebellum	SCAN
rs4802066	ITPKC	cis	cerebellum	SCAN
rs4802066	CEACAM16	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38105000-38112600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr19:38105000-38116000	Weak transcription	Right Ventricle	heart
3	chr19:38105200-38115000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38107800-38110600	ZNF genes & repeats	Liver	Liver
5	chr19:38108800-38110800	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:38109000-38110800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:38109200-38109400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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