Variant report

Variant	rs7248895
Chromosome Location	chr19:39524333-39524334
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	EP300	chr19:39524069-39524567	MCF-7	breast:	n/a	n/a
4	CTCF	chr19:39524260-39524410	HMEC	breast:	n/a	n/a
5	SIN3AK20	chr19:39524030-39524682	MCF-7	breast:	n/a	n/a
6	CTCF	chr19:39524220-39524370	MCF-7	breast:	n/a	n/a
7	POLR2A	chr19:39520454-39524689	PANC-1	pancreas:	n/a	n/a
8	REST	chr19:39524144-39524442	MCF-7	breast:	n/a	n/a
9	CEBPB	chr19:39523960-39524688	MCF-7	breast:	n/a	chr19:39524063-39524074
10	CTCF	chr19:39524260-39524410	HEEpiC	esophagus:	n/a	n/a
11	CTCF	chr19:39524300-39524450	HMEC	breast:	n/a	n/a
12	ZNF217	chr19:39524136-39524489	MCF-7	breast:	n/a	n/a
13	POLR2A	chr19:39519979-39524546	PANC-1	pancreas:	n/a	n/a
14	GATA3	chr19:39524146-39524550	MCF-7	breast:	n/a	n/a
15	NR2F2	chr19:39524117-39524598	MCF-7	breast:	n/a	n/a
16	FOXA1	chr19:39524214-39524434	T-47D	breast:	n/a	n/a
17	HDAC2	chr19:39524037-39524518	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: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10426382	0.91[EUR][1000 genomes]
rs12151095	0.93[EUR][1000 genomes]
rs12151101	0.87[EUR][1000 genomes]
rs12151263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151266	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151268	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151272	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55772809	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55773274	0.84[AMR][1000 genomes]
rs55785583	0.80[AMR][1000 genomes]
rs55854060	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55873651	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55894804	0.87[EUR][1000 genomes]
rs55919402	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55966336	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56063522	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56166490	0.83[AMR][1000 genomes]
rs56405021	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248416	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255339	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032408	0.80[AMR][1000 genomes]
rs73032437	0.80[AMR][1000 genomes]
rs73047948	0.88[AMR][1000 genomes]
rs73047959	0.80[AMR][1000 genomes]
rs73049875	0.80[AMR][1000 genomes]
rs73049881	0.80[AMR][1000 genomes]
rs8102539	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105813	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8107766	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107781	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108019	0.92[AMR][1000 genomes];0.87[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7248895	FBXO27	cis	Esophagus Mucosa	GTEx
rs7248895	CTB-189B5.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:31 , 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	chr19:39523400-39524400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:39523400-39524400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:39523400-39524400	Enhancers	Hela-S3	cervix
8	chr19:39523400-39524600	Enhancers	HepG2	liver
9	chr19:39523400-39524800	Enhancers	HMEC	breast
10	chr19:39523400-39525000	Enhancers	NHEK	skin
11	chr19:39523400-39529000	Weak transcription	Esophagus	oesophagus
12	chr19:39523400-39535400	Weak transcription	Right Atrium	heart
13	chr19:39523600-39524400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:39523600-39524600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:39523600-39524600	Enhancers	Fetal Intestine Small	intestine
16	chr19:39523600-39525000	Enhancers	Placenta	Placenta
17	chr19:39523600-39525200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr19:39523800-39524400	Enhancers	A549	lung
19	chr19:39523800-39524600	Enhancers	Osteobl	bone
20	chr19:39523800-39524800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:39523800-39524800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:39523800-39525000	Enhancers	Adipose Nuclei	Adipose
23	chr19:39523800-39525000	Enhancers	Fetal Intestine Large	intestine
24	chr19:39523800-39528400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr19:39523800-39528600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:39523800-39528600	Weak transcription	Brain Substantia Nigra	brain
27	chr19:39523800-39528800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:39523800-39528800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:39523800-39528800	Weak transcription	K562	blood
30	chr19:39524200-39524400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr19:39524200-39524400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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