Variant report

Variant	rs2823736
Chromosome Location	chr21:17658262-17658263
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	TEAD4	chr21:17658230-17658618	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr21:17657952-17658724	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr21:17658095-17658648	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr21:17658002-17658672	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr21:17658064-17658626	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr21:17658049-17658631	ECC-1	luminal epithelium:	n/a	n/a
8	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: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1492954	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492955	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492956	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151577	0.80[JPT][hapmap]
rs189457	0.85[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs239051	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs239055	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs239056	0.93[ASN][1000 genomes]
rs239060	0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs239063	0.87[ASN][1000 genomes]
rs239064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs239065	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2823735	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823737	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2823738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823741	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2823743	1.00[CEU][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs28483187	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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:36 , 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	chr21:17656800-17658400	Weak transcription	Adipose Nuclei	Adipose
7	chr21:17656800-17659200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr21:17656800-17663000	Weak transcription	Liver	Liver
9	chr21:17657000-17659400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr21:17657600-17658400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr21:17657600-17658600	Enhancers	Ovary	ovary
12	chr21:17657600-17659400	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr21:17657800-17658400	Enhancers	Fetal Muscle Leg	muscle
14	chr21:17657800-17658400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr21:17657800-17658400	Active TSS	Stomach Smooth Muscle	stomach
16	chr21:17657800-17658600	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr21:17657800-17658600	Enhancers	Fetal Kidney	kidney
18	chr21:17657800-17658600	Enhancers	Psoas Muscle	Psoas
19	chr21:17657800-17658800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr21:17657800-17658800	Enhancers	Fetal Lung	lung
21	chr21:17657800-17659200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr21:17657800-17659200	Enhancers	NH-A	brain
23	chr21:17658000-17658400	Enhancers	Fetal Brain Male	brain
24	chr21:17658000-17658600	Active TSS	Brain Hippocampus Middle	brain
25	chr21:17658000-17658600	Flanking Active TSS	Fetal Brain Female	brain
26	chr21:17658200-17658400	Enhancers	Esophagus	oesophagus
27	chr21:17658200-17658600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr21:17658200-17658600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr21:17658200-17658600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:17658200-17658600	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr21:17658200-17658600	Active TSS	Brain Cingulate Gyrus	brain
32	chr21:17658200-17658600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr21:17658200-17658600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr21:17658200-17658600	Active TSS	Brain Substantia Nigra	brain
35	chr21:17658200-17658600	Active TSS	Right Atrium	heart
36	chr21:17658200-17659000	Active TSS	Brain Anterior Caudate	brain

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