Variant report

Variant	rs4245766
Chromosome Location	chr2:31242194-31242195
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	chr2:31238924..31240507-chr2:31241595..31243780,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10164479	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs10166921	0.95[JPT][hapmap]
rs10174368	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10197865	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10198054	0.82[CEU][hapmap]
rs10206704	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10209881	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10865086	0.95[JPT][hapmap]
rs12473730	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12613732	0.82[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs12621546	0.82[CEU][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs12712300	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs12712304	0.84[MEX][hapmap]
rs12999804	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs13009779	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1862966	0.95[JPT][hapmap]
rs1862967	0.95[JPT][hapmap]
rs1862968	0.95[JPT][hapmap]
rs2113487	0.94[JPT][hapmap]
rs2113488	0.89[JPT][hapmap]
rs2194454	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2194455	0.82[CEU][hapmap]
rs2194456	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2216827	0.82[ASN][1000 genomes]
rs4245765	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951960	0.80[CHD][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs4952027	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4952028	0.95[JPT][hapmap]
rs4952031	0.95[JPT][hapmap]
rs5009910	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6543594	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6708989	0.94[JPT][hapmap]
rs6752303	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6752662	0.95[JPT][hapmap]
rs7579017	0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7582401	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs7601904	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7605643	0.95[JPT][hapmap]
rs7605982	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7608731	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs9308914	0.95[JPT][hapmap]
rs9679162	0.82[CHB][hapmap];0.95[JPT][hapmap]

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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4245766	FAM179A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31232600-31251000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:31235200-31251000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:31235400-31251000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:31236400-31249400	Weak transcription	NHEK	skin

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