Variant report

Variant	rs4559230
Chromosome Location	chr8:58654271-58654272
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	PBX3	chr8:58653786-58654683	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr8:58653780-58654828	SK-N-SH	brain:	n/a	chr8:58654649-58654659
3	GATA2	chr8:58653876-58654275	SH-SY5Y	brain:	n/a	n/a
4	GATA3	chr8:58653332-58654697	SK-N-SH	brain:	n/a	chr8:58654649-58654659
5	TCF12	chr8:58653248-58654682	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr8:58653924-58654758	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr8:58653215-58654813	SK-N-SH	brain:	n/a	n/a
8	EP300	chr8:58654159-58654569	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000254139	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10957018	0.82[ASN][1000 genomes]
rs4237018	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4237019	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4301443	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532583	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4560771	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4738615	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4738616	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4738617	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7000187	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7000215	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7000222	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533217	chr8:57991065-58789001	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv890937	chr8:58600994-58695807	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:58651800-58658600	Weak transcription	Gastric	stomach
2	chr8:58651800-58660400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:58652800-58654400	Enhancers	NHLF	lung
4	chr8:58652800-58655000	Enhancers	HSMM	muscle
5	chr8:58653000-58654400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr8:58653000-58654400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr8:58653000-58654600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:58653000-58654800	Enhancers	HSMMtube	muscle
9	chr8:58653000-58655000	Enhancers	NH-A	brain
10	chr8:58653200-58654400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr8:58653400-58654600	Enhancers	Fetal Stomach	stomach
12	chr8:58653400-58654800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr8:58653600-58654400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:58653800-58654400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr8:58653800-58658000	Weak transcription	HepG2	liver
16	chr8:58654000-58657800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr8:58654000-58657800	Weak transcription	Liver	Liver
18	chr8:58654000-58657800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr8:58654000-58657800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr8:58654200-58654600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr8:58654200-58654800	Enhancers	Osteobl	bone
22	chr8:58654200-58655000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr8:58654200-58656800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr8:58654200-58656800	Enhancers	NHDF-Ad	bronchial
25	chr8:58654200-58657800	Weak transcription	Adipose Nuclei	Adipose
26	chr8:58654200-58657800	Weak transcription	Colon Smooth Muscle	Colon
27	chr8:58654200-58657800	Weak transcription	Ovary	ovary
28	chr8:58654200-58657800	Weak transcription	Hela-S3	cervix
29	chr8:58654200-58658000	Weak transcription	Fetal Muscle Leg	muscle
30	chr8:58654200-58658000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr8:58654200-58658200	Weak transcription	Fetal Lung	lung
32	chr8:58654200-58658600	Weak transcription	Spleen	Spleen
33	chr8:58654200-58660400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links