Variant report

Variant	rs9493459
Chromosome Location	chr6:133155758-133155759
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133133823..133137064-chr6:133152471..133155832,4	K562	blood:

Variant related genes	Relation type
ENSG00000206754	Chromatin interaction
ENSG00000112306	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001018	0.85[ASN][1000 genomes]
rs1009687	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10872399	0.85[ASN][1000 genomes]
rs11154696	0.82[CHD][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs12192765	0.84[CHB][hapmap];0.87[ASN][1000 genomes]
rs12200907	0.81[CHD][hapmap]
rs12202302	0.89[CEU][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1359142	0.81[CHD][hapmap]
rs1408062	0.81[CHD][hapmap]
rs1408065	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1544060	0.87[ASN][1000 genomes]
rs1983607	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs271179	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3756969	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778174	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4895945	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4897617	0.81[CHD][hapmap]
rs4897619	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs528694	0.86[ASN][1000 genomes]
rs6569855	0.80[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6907421	0.80[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs6921262	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6926466	0.89[CEU][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6927761	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755894	0.87[ASN][1000 genomes]
rs761125	0.83[CEU][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7740291	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7756588	0.81[CHD][hapmap]
rs7768053	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs7768634	0.80[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs7774585	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs9321378	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9321379	0.85[ASN][1000 genomes]
rs9373030	0.81[CHD][hapmap]
rs9373033	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9375921	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9375927	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9385624	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9402461	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs9402465	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9493451	0.89[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9493458	0.86[ASW][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap]
rs9493464	0.86[ASN][1000 genomes]
rs9493468	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9493459	SNORA33	cis	cerebellum	SCAN
rs9493459	LOC285735	cis	parietal	SCAN
rs9493459	ACA33	cis	multi-tissue	Pritchard
rs9493459	TMEM200A	cis	cerebellum	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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