Variant report

Variant	rs6798952
Chromosome Location	chr3:54562556-54562557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11130423	0.85[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11707007	0.91[EUR][1000 genomes]
rs11708915	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711518	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs11714447	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13073425	0.91[EUR][1000 genomes]
rs13082611	0.83[CHB][hapmap]
rs13089488	0.91[EUR][1000 genomes]
rs17140	0.96[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2053862	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs28507696	0.89[EUR][1000 genomes]
rs2884804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs57828037	0.91[EUR][1000 genomes]
rs58452494	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414584	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445673	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6445677	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs6445680	0.92[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs6445682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs6445684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445687	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445690	0.96[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs6775352	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6789926	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap]
rs6790503	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7372541	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs7372624	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7373390	0.83[CHB][hapmap]
rs7373932	0.91[CHB][hapmap]
rs7374204	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7428361	0.92[EUR][1000 genomes]
rs7431090	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7432845	0.96[CEU][hapmap]
rs7433752	0.81[AMR][1000 genomes]
rs7636708	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816842	0.90[EUR][1000 genomes]
rs9855891	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs9874147	0.91[EUR][1000 genomes]
rs9874177	0.96[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9879189	0.91[CHB][hapmap];0.88[CHD][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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv876810	chr3:54480798-54585416	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6798952	C3orf51	cis	cerebellum	SCAN
rs6798952	DNASE1L3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54561200-54562800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:54561400-54563000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr3:54561600-54563000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr3:54561600-54563600	Enhancers	Hela-S3	cervix
5	chr3:54561800-54562800	Weak transcription	Right Atrium	heart
6	chr3:54561800-54564000	Weak transcription	Left Ventricle	heart
7	chr3:54561800-54564000	Weak transcription	Psoas Muscle	Psoas
8	chr3:54561800-54564000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:54562200-54563200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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