Variant report

Variant	rs11718240
Chromosome Location	chr3:24089253-24089254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24086798..24089297-chr3:24089834..24092711,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1133926	0.82[JPT][hapmap]
rs1136155	0.82[JPT][hapmap]
rs11705746	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11708328	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11709111	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11709760	0.89[EUR][1000 genomes]
rs11710679	0.82[JPT][hapmap]
rs11713246	0.82[JPT][hapmap]
rs11714770	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714787	0.89[EUR][1000 genomes]
rs11718625	0.82[JPT][hapmap]
rs11721182	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12497944	0.82[JPT][hapmap]
rs13318927	0.82[JPT][hapmap]
rs13325754	0.82[JPT][hapmap]
rs17014081	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014136	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17787211	0.82[JPT][hapmap]
rs2063480	0.88[CHB][hapmap];0.86[MEX][hapmap]
rs2063481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2089848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28503241	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28702740	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35316896	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4131864	0.82[JPT][hapmap]
rs4561770	0.88[CHB][hapmap]
rs6789983	0.82[JPT][hapmap]
rs73822696	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623641	0.88[CHB][hapmap]
rs7634184	0.88[CHB][hapmap]
rs7645692	0.84[EUR][1000 genomes]
rs8933	0.82[JPT][hapmap]
rs949715	0.89[EUR][1000 genomes]
rs9836970	0.82[JPT][hapmap]
rs9876561	0.82[JPT][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv834639	chr3:24037113-24233925	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1004037	chr3:24064777-24143719	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11718240	TOP2B	cis	cerebellum	SCAN
rs11718240	ART5	trans	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24079600-24090400	Weak transcription	Lung	lung
2	chr3:24084600-24089400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:24088200-24091400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:24088400-24091800	Enhancers	NHDF-Ad	bronchial
5	chr3:24088600-24089600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:24088600-24090600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:24088600-24090600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:24088600-24090800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:24088800-24089800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:24088800-24089800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:24088800-24090000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:24088800-24090600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:24088800-24090600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:24088800-24090600	Enhancers	Colon Smooth Muscle	Colon
15	chr3:24088800-24090600	Enhancers	Hela-S3	cervix
16	chr3:24088800-24090600	Enhancers	NHEK	skin
17	chr3:24088800-24090600	Enhancers	Osteobl	bone
18	chr3:24088800-24090800	Enhancers	Adipose Nuclei	Adipose
19	chr3:24088800-24090800	Enhancers	Placenta	Placenta
20	chr3:24088800-24090800	Enhancers	Ovary	ovary
21	chr3:24088800-24090800	Enhancers	HMEC	breast
22	chr3:24088800-24090800	Enhancers	NHLF	lung
23	chr3:24088800-24091400	Enhancers	HSMMtube	muscle
24	chr3:24089000-24089600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr3:24089000-24089800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr3:24089000-24089800	Enhancers	Psoas Muscle	Psoas
27	chr3:24089000-24089800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:24089000-24089800	Enhancers	A549	lung
29	chr3:24089000-24089800	Enhancers	HSMM	muscle
30	chr3:24089000-24090000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:24089000-24090600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:24089000-24090600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:24089000-24090600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:24089000-24090600	Enhancers	Aorta	Aorta
35	chr3:24089200-24089800	Enhancers	HUVEC	blood vessel
36	chr3:24089200-24089800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:24089200-24090400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:24089200-24090600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:24089200-24090600	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links