Variant report

Variant	rs7248652
Chromosome Location	chr19:39524172-39524173
allele	C/T
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	EP300	chr19:39524069-39524567	MCF-7	breast:	n/a	n/a
4	SIN3AK20	chr19:39524030-39524682	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:39520454-39524689	PANC-1	pancreas:	n/a	n/a
6	REST	chr19:39524144-39524442	MCF-7	breast:	n/a	n/a
7	CEBPB	chr19:39523960-39524688	MCF-7	breast:	n/a	chr19:39524063-39524074
8	CEBPB	chr19:39524002-39524190	A549	lung:	n/a	chr19:39524063-39524074
9	ZNF217	chr19:39524136-39524489	MCF-7	breast:	n/a	n/a
10	POLR2A	chr19:39519979-39524546	PANC-1	pancreas:	n/a	n/a
11	GATA3	chr19:39524146-39524550	MCF-7	breast:	n/a	n/a
12	NR2F2	chr19:39524117-39524598	MCF-7	breast:	n/a	n/a
13	HDAC2	chr19:39524037-39524518	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39464164..39468178-chr19:39520932..39524285,4	MCF-7	breast:

Variant related genes	Relation type
FBXO27	TF binding region
ENSG00000269190	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10406222	0.90[ASN][1000 genomes]
rs10416823	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417436	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424632	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10424827	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426645	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426661	0.88[ASN][1000 genomes]
rs1062261	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10853723	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10853724	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083499	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083500	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083501	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083502	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1139251	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11667641	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670486	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670520	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11673044	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11673637	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11880441	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883422	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609806	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610200	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12610248	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12971842	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12972850	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12972978	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978163	0.90[ASN][1000 genomes]
rs12978749	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982199	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12982349	0.92[ASN][1000 genomes]
rs12982529	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12985447	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1651748	0.84[EUR][1000 genomes]
rs1840745	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840746	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840747	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840748	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864191	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1869983	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36154890	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848623	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4280369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802007	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802009	0.87[ASN][1000 genomes]
rs4803181	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803185	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803186	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803187	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803188	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803193	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58897626	0.89[ASN][1000 genomes]
rs60775146	0.89[ASN][1000 genomes]
rs62119538	0.90[ASN][1000 genomes]
rs628335	0.87[ASN][1000 genomes]
rs6508835	0.89[ASN][1000 genomes]
rs6508836	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508837	0.89[ASN][1000 genomes]
rs6508838	0.92[ASN][1000 genomes]
rs6508839	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508840	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508841	0.92[ASN][1000 genomes]
rs6508842	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508843	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681496	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247801	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250110	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250431	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251264	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255211	0.93[ASN][1000 genomes]
rs7256126	0.91[ASN][1000 genomes]
rs7258862	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259064	0.88[ASN][1000 genomes]
rs7259197	0.88[ASN][1000 genomes]
rs7259473	0.81[ASN][1000 genomes]
rs7259801	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8100503	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103187	0.88[ASN][1000 genomes]
rs8104751	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104899	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104990	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105865	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109176	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7248652	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs7248652	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs7248652	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7248652	FBXO27	cis	Esophagus Mucosa	GTEx

Chromatin state (count:33 , 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	chr19:39523200-39524400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr19:39523200-39524400	Enhancers	NH-A	brain
5	chr19:39523400-39524200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:39523400-39524400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:39523400-39524400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:39523400-39524400	Enhancers	Hela-S3	cervix
9	chr19:39523400-39524600	Enhancers	HepG2	liver
10	chr19:39523400-39524800	Enhancers	HMEC	breast
11	chr19:39523400-39525000	Enhancers	NHEK	skin
12	chr19:39523400-39529000	Weak transcription	Esophagus	oesophagus
13	chr19:39523400-39535400	Weak transcription	Right Atrium	heart
14	chr19:39523600-39524200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:39523600-39524400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:39523600-39524600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:39523600-39524600	Enhancers	Fetal Intestine Small	intestine
18	chr19:39523600-39525000	Enhancers	Placenta	Placenta
19	chr19:39523600-39525200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:39523800-39524400	Enhancers	A549	lung
21	chr19:39523800-39524600	Enhancers	Osteobl	bone
22	chr19:39523800-39524800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:39523800-39524800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:39523800-39525000	Enhancers	Adipose Nuclei	Adipose
25	chr19:39523800-39525000	Enhancers	Fetal Intestine Large	intestine
26	chr19:39523800-39528400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:39523800-39528600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:39523800-39528600	Weak transcription	Brain Substantia Nigra	brain
29	chr19:39523800-39528800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:39523800-39528800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:39523800-39528800	Weak transcription	K562	blood
32	chr19:39524000-39524200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:39524000-39524200	Bivalent/Poised TSS	NHDF-Ad	bronchial

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