Variant report

Variant	rs9672559
Chromosome Location	chr15:74991336-74991337
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	chr15:74989524..74991754-chr15:75083871..75085469,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10459601	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs10459648	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs10851873	0.86[JPT][hapmap]
rs11072492	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs11072493	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs11072494	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072495	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072496	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072497	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072498	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072499	0.82[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs11629749	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11629946	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap]
rs12439113	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12441932	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12442097	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs1456432	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2068982	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2198843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2415242	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2415245	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3826041	0.84[ASN][1000 genomes]
rs4073149	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs4886601	0.89[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4887159	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs4887163	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs4887166	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58473469	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6495112	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs6495116	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs6495117	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6495118	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495119	0.82[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs6495121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7161903	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7171838	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7176095	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7178568	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap]
rs74025818	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7495708	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7497036	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs7497342	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8023479	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs8026923	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs8027066	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs8028430	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs8029116	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs8029215	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs9635320	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.81[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	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv817698	chr15:74889163-75019449	Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9672559	SEMA7A	cis	cerebellum	SCAN
rs9672559	SCAMP5	cis	parietal	SCAN
rs9672559	CELF6	cis	cerebellum	SCAN
rs9672559	ARIH1	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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