Variant report

Variant	rs561148
Chromosome Location	chr19:39524585-39524586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr19:39524088-39524603	MCF-7	breast:	n/a	n/a
2	CEBPB	chr19:39523985-39524706	MCF-7	breast:	n/a	chr19:39524063-39524074
3	SIN3AK20	chr19:39524030-39524682	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:39520454-39524689	PANC-1	pancreas:	n/a	n/a
5	CEBPB	chr19:39523960-39524688	MCF-7	breast:	n/a	chr19:39524063-39524074
6	CEBPB	chr19:39524585-39524632	A549	lung:	n/a	n/a
7	NR2F2	chr19:39524117-39524598	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39520644..39523609-chr19:39524329..39528239,4	K562	blood:

Variant related genes	Relation type
FBXO27	TF binding region
ENSG00000267992	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10409280	0.81[ASN][1000 genomes]
rs10411234	0.89[ASN][1000 genomes]
rs10411271	0.81[ASN][1000 genomes]
rs12463075	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12609401	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974080	0.88[ASN][1000 genomes]
rs12974708	0.80[ASN][1000 genomes]
rs12975482	0.82[ASN][1000 genomes]
rs12976100	0.80[ASN][1000 genomes]
rs12979968	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981133	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982067	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12983352	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13345897	0.83[ASN][1000 genomes]
rs1626050	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1627631	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1628376	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1628426	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1629253	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1651747	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16973058	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864186	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1864188	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1869982	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2318897	0.83[ASN][1000 genomes]
rs34240661	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35000840	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35622111	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35940388	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802010	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs487356	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs516901	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523890	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs523943	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs542464	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553330	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs554932	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561329	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572764	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57401831	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57724551	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs582575	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582593	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583529	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583995	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs584806	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs584822	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586107	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs586176	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59698424	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs598468	0.94[ASN][1000 genomes]
rs599230	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs602899	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61553368	0.91[ASN][1000 genomes]
rs618068	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62119464	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62119508	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62119510	0.90[ASN][1000 genomes]
rs62121529	0.81[EUR][1000 genomes]
rs62121530	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62121532	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs662202	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs678772	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs678848	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679657	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679732	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246076	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930100	0.82[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs561148	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39523000-39524600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:39523000-39524600	Enhancers	Liver	Liver
3	chr19:39523400-39524600	Enhancers	HepG2	liver
4	chr19:39523400-39524800	Enhancers	HMEC	breast
5	chr19:39523400-39525000	Enhancers	NHEK	skin
6	chr19:39523400-39529000	Weak transcription	Esophagus	oesophagus
7	chr19:39523400-39535400	Weak transcription	Right Atrium	heart
8	chr19:39523600-39524600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:39523600-39524600	Enhancers	Fetal Intestine Small	intestine
10	chr19:39523600-39525000	Enhancers	Placenta	Placenta
11	chr19:39523600-39525200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:39523800-39524600	Enhancers	Osteobl	bone
13	chr19:39523800-39524800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:39523800-39524800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:39523800-39525000	Enhancers	Adipose Nuclei	Adipose
16	chr19:39523800-39525000	Enhancers	Fetal Intestine Large	intestine
17	chr19:39523800-39528400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:39523800-39528600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39523800-39528600	Weak transcription	Brain Substantia Nigra	brain
20	chr19:39523800-39528800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:39523800-39528800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:39523800-39528800	Weak transcription	K562	blood
23	chr19:39524400-39527400	Weak transcription	A549	lung
24	chr19:39524400-39528600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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