Variant report

Variant	rs9402461
Chromosome Location	chr6:133164442-133164443
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	chr6:133132907..133137002-chr6:133163874..133168278,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206754	Chromatin interaction
ENSG00000112306	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1001018	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009687	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10872399	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1124450	0.84[CHB][hapmap];0.84[CHD][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs12192765	0.85[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12193918	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs12200907	0.84[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs12202302	0.91[CHD][hapmap]
rs1359142	0.84[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs1408062	0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs1408063	0.80[ASN][1000 genomes]
rs1408065	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs1544060	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1965895	0.81[ASN][1000 genomes]
rs271179	0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4895945	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4897617	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs4897619	0.81[ASN][1000 genomes]
rs528694	0.81[ASN][1000 genomes]
rs6569855	0.95[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569857	0.81[ASN][1000 genomes]
rs6569858	0.81[ASN][1000 genomes]
rs6569859	0.81[ASN][1000 genomes]
rs6907421	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6921262	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6925225	0.81[ASN][1000 genomes]
rs6926466	0.91[CHD][hapmap]
rs6927761	0.88[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs755894	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs761125	0.82[CHD][hapmap]
rs7740291	0.85[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs7743635	0.80[ASN][1000 genomes]
rs7744235	0.80[ASN][1000 genomes]
rs7751333	0.81[ASN][1000 genomes]
rs7751359	0.81[ASN][1000 genomes]
rs7755422	0.81[ASN][1000 genomes]
rs7756588	0.84[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs7759900	0.81[ASN][1000 genomes]
rs7764252	0.80[ASN][1000 genomes]
rs7766944	0.81[ASN][1000 genomes]
rs7768053	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768470	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs7768634	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7774585	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321378	0.89[ASN][1000 genomes]
rs9321379	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321380	0.81[ASN][1000 genomes]
rs9373030	0.84[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs9373033	0.85[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9375924	0.80[ASN][1000 genomes]
rs9375925	0.80[ASN][1000 genomes]
rs9375927	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs9385624	0.85[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9402460	0.81[ASN][1000 genomes]
rs9402462	0.80[ASN][1000 genomes]
rs9402465	0.81[ASN][1000 genomes]
rs9493450	0.80[CHD][hapmap]
rs9493459	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]
rs9493464	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9493468	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9402461	ACA33	cis	multi-tissue	Pritchard
rs9402461	LOC285735	cis	parietal	SCAN
rs9402461	SNORA33	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133163600-133165000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:133164000-133165600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:133164400-133165400	Enhancers	HUES64 Cell Line	embryonic stem cell

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