Variant report

Variant	rs11939449
Chromosome Location	chr4:78356862-78356863
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	chr4:78287359..78291622-chr4:78351702..78357008,5	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10008817	0.88[CEU][hapmap];0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs10017843	0.88[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[ASN][1000 genomes]
rs11931577	0.82[CHD][hapmap]
rs11934887	0.82[CHD][hapmap]
rs11936072	0.87[CEU][hapmap];0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs11936117	0.88[CEU][hapmap]
rs11942781	0.88[CEU][hapmap]
rs11945282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11946102	0.88[CEU][hapmap];0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs17002675	0.88[CEU][hapmap]
rs17002676	0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.90[ASN][1000 genomes]
rs17002681	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17002682	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17002687	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17002700	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs1867107	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1992489	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2083701	0.93[CEU][hapmap]
rs2083702	0.89[EUR][1000 genomes]
rs2866292	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35848195	0.90[ASN][1000 genomes]
rs4152	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859499	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4859839	0.88[CEU][hapmap];0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs4859840	0.88[CEU][hapmap];0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs4859842	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859843	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859844	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859845	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859846	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55685718	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55729445	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55915318	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56092580	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56107646	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56164638	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60688594	0.90[ASN][1000 genomes]
rs62302403	0.90[ASN][1000 genomes]
rs62302404	0.90[ASN][1000 genomes]
rs62302406	0.90[ASN][1000 genomes]
rs62302436	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62302437	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62302438	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62302439	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62302442	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62302445	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6826277	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs72650458	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7670432	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7681293	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7699486	0.81[AMR][1000 genomes];0.89[EUR][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	nsv829974	chr4:78240718-78415642	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11939449	SEPT11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78354400-78357600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr4:78356000-78357400	Enhancers	Spleen	Spleen
3	chr4:78356600-78357400	Enhancers	Aorta	Aorta
4	chr4:78356800-78357400	Enhancers	Ovary	ovary
5	chr4:78356800-78357600	Enhancers	Fetal Lung	lung
6	chr4:78356800-78358000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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