Variant report

Variant	rs60775146
Chromosome Location	chr19:39546272-39546273
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39523038..39525011-chr19:39545332..39547051,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10406222	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10411271	0.89[AFR][1000 genomes]
rs10416823	0.89[ASN][1000 genomes]
rs10417436	0.89[ASN][1000 genomes]
rs10424827	0.90[ASN][1000 genomes]
rs10426645	0.88[ASN][1000 genomes]
rs10426661	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853723	0.81[ASN][1000 genomes]
rs10853724	0.89[ASN][1000 genomes]
rs11083499	0.87[ASN][1000 genomes]
rs11083500	0.88[ASN][1000 genomes]
rs11083501	0.89[ASN][1000 genomes]
rs11083502	0.88[ASN][1000 genomes]
rs11667641	0.87[ASN][1000 genomes]
rs11670486	0.88[ASN][1000 genomes]
rs11670520	0.85[ASN][1000 genomes]
rs11880441	0.89[ASN][1000 genomes]
rs11883422	0.91[ASN][1000 genomes]
rs12609806	0.87[ASN][1000 genomes]
rs12971842	0.84[ASN][1000 genomes]
rs12972850	0.87[ASN][1000 genomes]
rs12972978	0.87[ASN][1000 genomes]
rs12978163	0.81[ASN][1000 genomes]
rs12978749	0.87[ASN][1000 genomes]
rs12982349	0.83[ASN][1000 genomes]
rs12982529	0.85[ASN][1000 genomes]
rs12985447	0.85[ASN][1000 genomes]
rs13345897	0.85[AFR][1000 genomes]
rs1840745	0.89[ASN][1000 genomes]
rs1840746	0.87[ASN][1000 genomes]
rs1840747	0.87[ASN][1000 genomes]
rs1840748	0.88[ASN][1000 genomes]
rs1864191	0.89[ASN][1000 genomes]
rs1869983	0.91[ASN][1000 genomes]
rs2318897	0.90[AFR][1000 genomes]
rs36154890	0.89[ASN][1000 genomes]
rs3848623	0.87[ASN][1000 genomes]
rs4280369	0.89[ASN][1000 genomes]
rs4803185	0.89[ASN][1000 genomes]
rs4803186	0.89[ASN][1000 genomes]
rs4803187	0.89[ASN][1000 genomes]
rs4803188	0.90[ASN][1000 genomes]
rs4803193	0.91[ASN][1000 genomes]
rs58897626	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119538	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628335	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508836	0.81[ASN][1000 genomes]
rs6508838	0.83[ASN][1000 genomes]
rs6508839	0.85[ASN][1000 genomes]
rs6508840	0.85[ASN][1000 genomes]
rs6508841	0.83[ASN][1000 genomes]
rs6508842	0.89[ASN][1000 genomes]
rs6508843	0.89[ASN][1000 genomes]
rs681496	0.85[ASN][1000 genomes]
rs7247801	0.89[ASN][1000 genomes]
rs7248513	0.89[ASN][1000 genomes]
rs7248652	0.89[ASN][1000 genomes]
rs7250110	0.86[ASN][1000 genomes]
rs7250431	0.91[ASN][1000 genomes]
rs7251264	0.91[ASN][1000 genomes]
rs7255211	0.84[ASN][1000 genomes]
rs7256126	0.82[ASN][1000 genomes]
rs7258862	0.90[ASN][1000 genomes]
rs7259064	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259197	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259801	0.87[ASN][1000 genomes]
rs8104751	0.89[ASN][1000 genomes]
rs8104899	0.89[ASN][1000 genomes]
rs8104990	0.89[ASN][1000 genomes]
rs8105865	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs60775146	FBXO27	cis	Esophagus Mucosa	GTEx
rs60775146	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs60775146	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs60775146	CTB-189B5.3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39541200-39546400	Weak transcription	Right Atrium	heart
2	chr19:39542200-39546600	Enhancers	Fetal Intestine Large	intestine
3	chr19:39544800-39546800	Enhancers	HepG2	liver
4	chr19:39545200-39564400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:39545600-39546400	Weak transcription	Stomach Mucosa	stomach
6	chr19:39545600-39546600	Enhancers	Fetal Intestine Small	intestine
7	chr19:39545600-39552000	Weak transcription	A549	lung
8	chr19:39545600-39560400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:39545800-39553600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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