Variant report

Variant	rs9993426
Chromosome Location	chr4:79875172-79875173
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79874766..79875467-chr4:81136378..81137184,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10018189	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10025599	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10034295	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11722437	1.00[ASN][1000 genomes]
rs1275046	0.80[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1275047	0.80[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs13108247	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1383425	0.96[ASN][1000 genomes]
rs1383426	0.95[ASN][1000 genomes]
rs1480718	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1480733	0.96[ASN][1000 genomes]
rs1825022	0.96[ASN][1000 genomes]
rs1979444	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs2046104	0.98[ASN][1000 genomes]
rs2288254	0.85[CHB][hapmap]
rs3822106	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs3937772	0.88[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4512020	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4576033	0.96[ASN][1000 genomes]
rs62308043	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6534083	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6534085	0.82[ASN][1000 genomes]
rs6534086	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6534087	0.82[ASN][1000 genomes]
rs6534090	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6846743	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6854347	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs725500	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7656083	0.82[ASN][1000 genomes]
rs7688534	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs931149	1.00[ASN][1000 genomes]
rs931150	1.00[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	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9993426	BMP3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79870400-79881600	Weak transcription	Aorta	Aorta
2	chr4:79873600-79877600	Weak transcription	Fetal Heart	heart
3	chr4:79873800-79878000	Weak transcription	Fetal Brain Female	brain
4	chr4:79874600-79875400	Enhancers	Fetal Muscle Leg	muscle

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