Variant report

Variant	rs10409280
Chromosome Location	chr19:39546960-39546961
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	chr19:39523038..39525011-chr19:39545332..39547051,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10411234	0.90[ASN][1000 genomes]
rs10411271	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151099	0.91[ASN][1000 genomes]
rs12463075	0.80[ASN][1000 genomes]
rs12609401	0.82[ASN][1000 genomes]
rs12974080	0.91[ASN][1000 genomes]
rs12974708	0.98[ASN][1000 genomes]
rs12975482	0.98[ASN][1000 genomes]
rs12976100	0.98[ASN][1000 genomes]
rs12979968	0.84[ASN][1000 genomes]
rs12981133	0.82[ASN][1000 genomes]
rs12982067	0.87[ASN][1000 genomes]
rs12983005	0.93[ASN][1000 genomes]
rs12983352	0.88[ASN][1000 genomes]
rs12983682	0.92[ASN][1000 genomes]
rs12984833	0.97[ASN][1000 genomes]
rs12984836	0.97[ASN][1000 genomes]
rs13345897	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1626050	0.83[ASN][1000 genomes]
rs1627631	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1628376	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1628426	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1629253	0.83[ASN][1000 genomes]
rs1651747	0.83[ASN][1000 genomes]
rs1654336	0.81[JPT][hapmap]
rs16973058	0.83[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs17795157	0.80[JPT][hapmap]
rs1864186	0.86[ASN][1000 genomes]
rs1864188	0.86[ASN][1000 genomes]
rs1869982	0.86[ASN][1000 genomes]
rs2318897	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562330	0.80[JPT][hapmap]
rs34240661	0.86[ASN][1000 genomes]
rs35622111	0.81[ASN][1000 genomes]
rs4802010	0.84[ASN][1000 genomes]
rs482342	0.80[JPT][hapmap]
rs483359	0.81[JPT][hapmap]
rs487356	0.83[ASN][1000 genomes]
rs498586	0.81[JPT][hapmap]
rs500660	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs500691	0.85[JPT][hapmap]
rs516901	0.83[ASN][1000 genomes]
rs523890	0.86[ASN][1000 genomes]
rs523943	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs542464	0.81[ASN][1000 genomes]
rs553330	0.83[ASN][1000 genomes]
rs554932	0.83[ASN][1000 genomes]
rs561148	0.81[ASN][1000 genomes]
rs561329	0.81[ASN][1000 genomes]
rs564474	0.81[JPT][hapmap]
rs572764	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs57401831	0.80[ASN][1000 genomes]
rs57724551	0.84[ASN][1000 genomes]
rs582575	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs582593	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs583529	0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs583995	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs584806	0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs584822	0.82[ASN][1000 genomes]
rs586107	0.80[ASN][1000 genomes]
rs586176	0.83[ASN][1000 genomes]
rs59698424	0.82[ASN][1000 genomes]
rs598468	0.85[ASN][1000 genomes]
rs599230	0.83[ASN][1000 genomes]
rs602899	0.83[ASN][1000 genomes]
rs61553368	0.89[ASN][1000 genomes]
rs618068	0.83[ASN][1000 genomes]
rs62119464	0.84[ASN][1000 genomes]
rs62119508	0.83[ASN][1000 genomes]
rs62119510	0.90[ASN][1000 genomes]
rs662202	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs678772	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs678848	0.83[ASN][1000 genomes]
rs678885	0.80[JPT][hapmap]
rs679657	0.83[ASN][1000 genomes]
rs679732	0.83[ASN][1000 genomes]
rs681145	0.81[JPT][hapmap]
rs930100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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
rs10409280	FBXO27	cis	Esophagus Mucosa	GTEx
rs10409280	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs10409280	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10409280	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39545200-39564400	Weak transcription	Brain Substantia Nigra	brain
2	chr19:39545600-39552000	Weak transcription	A549	lung
3	chr19:39545600-39560400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:39545800-39553600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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