Variant report

Variant	rs4097643
Chromosome Location	chr9:86110338-86110339
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:68818204..68820829-chr9:86108708..86111031,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11789184	0.91[ASN][1000 genomes]
rs11795151	0.95[ASN][1000 genomes]
rs34077008	0.91[ASN][1000 genomes]
rs3860934	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3860940	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3860941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3860942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4097644	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4111744	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4263845	0.89[ASN][1000 genomes]
rs4363276	0.95[ASN][1000 genomes]
rs4424349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4877783	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4877786	0.95[ASN][1000 genomes]
rs5028328	0.89[ASN][1000 genomes]
rs6559728	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7037642	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7042568	0.95[ASN][1000 genomes]
rs7043391	0.95[ASN][1000 genomes]
rs7043575	0.91[ASN][1000 genomes]
rs7046729	0.91[ASN][1000 genomes]
rs7862471	0.95[ASN][1000 genomes]
rs7863618	0.91[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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
2	nsv1038884	chr9:86089963-86215800	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4097643	SNTG1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86107200-86115200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:86107200-86123000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr9:86107600-86118600	Weak transcription	Ovary	ovary
4	chr9:86107800-86118400	Weak transcription	Left Ventricle	heart
5	chr9:86107800-86118600	Weak transcription	Right Atrium	heart
6	chr9:86108000-86120200	Weak transcription	Psoas Muscle	Psoas
7	chr9:86108000-86120200	Weak transcription	Right Ventricle	heart
8	chr9:86109000-86114400	Weak transcription	Hela-S3	cervix
9	chr9:86110200-86110800	Enhancers	NHDF-Ad	bronchial

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