Variant report

Variant	rs1533294
Chromosome Location	chr4:90048122-90048123
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	POLR2A	chr4:90047588-90048152	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90033016..90036136-chr4:90045912..90049753,4	K562	blood:
2	chr4:90043393..90046238-chr4:90047056..90051826,4	K562	blood:

Variant related genes	Relation type
RNU6-907P	TF binding region
ENSG00000180346	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10001420	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10028121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10033476	0.82[CHB][hapmap]
rs10433881	0.96[ASN][1000 genomes]
rs11734924	0.96[ASN][1000 genomes]
rs12645173	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12647095	0.96[ASN][1000 genomes]
rs12649875	0.96[ASN][1000 genomes]
rs13105546	0.96[ASN][1000 genomes]
rs13133608	0.96[ASN][1000 genomes]
rs13138927	0.93[ASN][1000 genomes]
rs1355836	0.85[ASN][1000 genomes]
rs1355837	0.85[ASN][1000 genomes]
rs1398937	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1398938	1.00[JPT][hapmap]
rs1398939	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1398941	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1398943	0.85[ASN][1000 genomes]
rs1513811	0.85[ASN][1000 genomes]
rs1513812	0.85[ASN][1000 genomes]
rs1513823	0.85[ASN][1000 genomes]
rs1533288	0.81[ASN][1000 genomes]
rs1533289	0.85[ASN][1000 genomes]
rs1708659	0.85[ASN][1000 genomes]
rs1708671	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1708672	0.81[ASN][1000 genomes]
rs1708673	1.00[JPT][hapmap]
rs1708683	0.85[ASN][1000 genomes]
rs1795735	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1795737	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1795740	1.00[JPT][hapmap]
rs1828735	0.85[ASN][1000 genomes]
rs1903004	1.00[CHB][hapmap]
rs1903009	1.00[CHB][hapmap]
rs1996139	0.85[ASN][1000 genomes]
rs2102650	0.92[ASN][1000 genomes]
rs2125410	1.00[CHB][hapmap]
rs2446309	1.00[CHB][hapmap]
rs2464526	1.00[CHB][hapmap]
rs2609266	1.00[CHB][hapmap]
rs2609274	1.00[CHB][hapmap]
rs2670618	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2670619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2670620	1.00[JPT][hapmap]
rs2670627	0.85[ASN][1000 genomes]
rs2670628	0.85[ASN][1000 genomes]
rs2704580	0.81[ASN][1000 genomes]
rs2704585	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2704588	1.00[CHB][hapmap]
rs2704592	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2869989	0.92[ASN][1000 genomes]
rs28718401	0.85[ASN][1000 genomes]
rs2904264	0.92[ASN][1000 genomes]
rs4325981	0.93[ASN][1000 genomes]
rs4693987	0.93[ASN][1000 genomes]
rs6532100	0.85[ASN][1000 genomes]
rs6532113	0.96[ASN][1000 genomes]
rs6823241	0.96[ASN][1000 genomes]
rs6826482	0.92[ASN][1000 genomes]
rs6834297	0.85[ASN][1000 genomes]
rs6843986	0.82[ASN][1000 genomes]
rs6845264	0.92[ASN][1000 genomes]
rs6846010	0.89[ASN][1000 genomes]
rs7657630	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7687207	0.82[AMR][1000 genomes]
rs8180333	0.85[ASN][1000 genomes]
rs922027	1.00[CHB][hapmap]
rs9307063	0.96[ASN][1000 genomes]
rs938265	0.85[ASN][1000 genomes]
rs938267	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs987314	0.81[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90049200	Weak transcription	Gastric	stomach
4	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
5	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:90042600-90049600	Enhancers	Fetal Intestine Small	intestine
7	chr4:90043400-90050200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:90044800-90056000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:90046000-90056200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:90047600-90055800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:90047800-90049000	Weak transcription	A549	lung
12	chr4:90047800-90050200	Weak transcription	HepG2	liver

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