Variant report

Variant	rs3904187
Chromosome Location	chr9:86009746-86009747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86009690..86011505-chr9:86151453..86153248,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10117284	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10125072	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11140060	0.85[ASN][1000 genomes]
rs12349789	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13299648	0.91[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28585601	0.85[ASN][1000 genomes]
rs3849865	0.84[ASN][1000 genomes]
rs3860901	0.81[CHD][hapmap];0.80[TSI][hapmap]
rs3860905	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3860906	0.85[ASN][1000 genomes]
rs3860907	0.85[ASN][1000 genomes]
rs3860909	0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3860912	0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3860913	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3860914	0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3904189	0.87[ASN][1000 genomes]
rs4478644	0.86[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4877756	0.82[CHD][hapmap]
rs4877757	0.82[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs7019165	0.87[ASN][1000 genomes]
rs7037795	0.85[ASN][1000 genomes]
rs7037928	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3904187	NTRK2	cis	cerebellum	SCAN
rs3904187	ISCA1	cis	parietal	SCAN
rs3904187	TDRD9	trans	parietal	SCAN
rs3904187	TLE1	cis	parietal	SCAN
rs3904187	TLE4	cis	parietal	SCAN
rs3904187	C9orf64	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86000000-86020600	Weak transcription	Fetal Brain Female	brain
2	chr9:86004600-86014200	Weak transcription	Gastric	stomach
3	chr9:86005400-86021000	Weak transcription	Right Atrium	heart
4	chr9:86007200-86013000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:86007400-86012000	Weak transcription	Left Ventricle	heart
6	chr9:86008000-86011600	Weak transcription	HepG2	liver

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