Variant report

Variant	rs239051
Chromosome Location	chr21:17658668-17658669
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	EP300	chr21:17658116-17658717	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr21:17657952-17658724	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr21:17658002-17658672	ECC-1	luminal epithelium:	n/a	n/a
4	FOXM1	chr21:17658001-17658754	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000201025	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1492954	0.91[ASN][1000 genomes]
rs1492955	0.91[ASN][1000 genomes]
rs1492956	0.91[ASN][1000 genomes]
rs151577	0.82[YRI][hapmap]
rs189457	0.92[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239055	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs239056	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs239060	0.84[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239062	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs239063	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239064	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs239065	0.92[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2823735	0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2823736	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2823737	0.91[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2823738	0.85[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2823741	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs28483187	0.90[ASN][1000 genomes]
rs9305762	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834051	chr21:17564843-17721764	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17634800-17667000	Weak transcription	Hela-S3	cervix
2	chr21:17653200-17659200	Weak transcription	Aorta	Aorta
3	chr21:17653600-17659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr21:17653800-17659000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr21:17654800-17666600	Weak transcription	Fetal Heart	heart
6	chr21:17656800-17659200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr21:17656800-17663000	Weak transcription	Liver	Liver
8	chr21:17657000-17659400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr21:17657600-17659400	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr21:17657800-17658800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr21:17657800-17658800	Enhancers	Fetal Lung	lung
12	chr21:17657800-17659200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:17657800-17659200	Enhancers	NH-A	brain
14	chr21:17658200-17659000	Active TSS	Brain Anterior Caudate	brain
15	chr21:17658400-17659200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr21:17658400-17670200	Weak transcription	Fetal Muscle Leg	muscle
17	chr21:17658600-17658800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr21:17658600-17658800	Weak transcription	Brain Substantia Nigra	brain
19	chr21:17658600-17658800	Enhancers	Fetal Brain Male	brain
20	chr21:17658600-17658800	Enhancers	Fetal Brain Female	brain
21	chr21:17658600-17659000	Weak transcription	Adipose Nuclei	Adipose
22	chr21:17658600-17659400	Enhancers	Brain Germinal Matrix	brain
23	chr21:17658600-17659400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr21:17658600-17659600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr21:17658600-17659600	Enhancers	Brain Angular Gyrus	brain
26	chr21:17658600-17659600	Enhancers	Brain Cingulate Gyrus	brain
27	chr21:17658600-17660000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr21:17658600-17674800	Weak transcription	Brain Hippocampus Middle	brain
29	chr21:17658600-17675200	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links