Variant report

Variant	rs1491166
Chromosome Location	chr3:56570097-56570098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56569030..56570634-chr3:56588357..56591686,3	K562	blood:

Variant related genes	Relation type
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10212341	0.84[MEX][hapmap]
rs10222449	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10222462	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1045926	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs10865998	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865999	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs11130536	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs11130538	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs11706624	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715395	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs11921326	0.83[ASN][1000 genomes]
rs12490749	0.83[ASN][1000 genomes]
rs12636392	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12636773	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12715490	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13094666	0.81[ASN][1000 genomes]
rs13097030	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352766	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1388251	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17056878	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17216740	0.82[ASN][1000 genomes]
rs2004199	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2029464	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs2035798	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2054987	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054988	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291499	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs2291501	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs2317133	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs2317245	0.83[ASN][1000 genomes]
rs28407059	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732512	0.83[ASN][1000 genomes]
rs4093514	0.90[EUR][1000 genomes]
rs4681746	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4681951	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681963	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs4974220	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974224	0.90[EUR][1000 genomes]
rs6765870	0.89[EUR][1000 genomes]
rs6774323	0.81[ASN][1000 genomes]
rs6784100	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6785479	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6798118	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6799576	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802051	0.83[ASN][1000 genomes]
rs6805469	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72877266	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7612599	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs7618024	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap]
rs7626378	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629559	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7646924	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7647272	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9811046	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9820759	0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs9822876	0.88[CHD][hapmap]
rs9836539	0.82[EUR][1000 genomes]
rs9840528	0.89[CEU][hapmap]
rs9842283	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs9845096	0.82[ASN][1000 genomes]
rs9845655	0.80[ASN][1000 genomes]
rs9846282	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9858728	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs9862490	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9881005	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9881789	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9881961	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9985253	0.95[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9985254	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][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	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1491166	ERC2	cis	cerebellum	SCAN
rs1491166	CCDC66	cis	cerebellum	SCAN
rs1491166	C3orf51	cis	cerebellum	SCAN
rs1491166	STAB1	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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