Variant report

Variant	rs2823735
Chromosome Location	chr21:17657785-17657786
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1492954	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492955	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492956	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151577	0.80[JPT][hapmap]
rs189457	0.85[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs239051	0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs239055	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs239056	0.94[ASN][1000 genomes]
rs239060	0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs239063	0.88[ASN][1000 genomes]
rs239064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239065	0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2823736	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];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2823738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[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];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28483187	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823735	C21orf91	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17634800-17667000	Weak transcription	Hela-S3	cervix
2	chr21:17649400-17657800	Weak transcription	Esophagus	oesophagus
3	chr21:17653200-17658200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr21:17653200-17659200	Weak transcription	Aorta	Aorta
5	chr21:17653400-17657800	Weak transcription	Fetal Muscle Leg	muscle
6	chr21:17653400-17658000	Weak transcription	HSMMtube	muscle
7	chr21:17653400-17658200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr21:17653600-17659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:17653800-17659000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr21:17654000-17657800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr21:17654200-17657800	Weak transcription	Fetal Lung	lung
12	chr21:17654200-17658200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr21:17654800-17657800	Weak transcription	Fetal Kidney	kidney
14	chr21:17654800-17658000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr21:17654800-17666600	Weak transcription	Fetal Heart	heart
16	chr21:17655000-17657800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr21:17655000-17657800	Weak transcription	Psoas Muscle	Psoas
18	chr21:17655200-17657800	Enhancers	Brain Substantia Nigra	brain
19	chr21:17655200-17657800	Weak transcription	NH-A	brain
20	chr21:17655800-17658200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr21:17656000-17658200	Enhancers	Brain Angular Gyrus	brain
22	chr21:17656600-17657800	Enhancers	Fetal Brain Male	brain
23	chr21:17656800-17657800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr21:17656800-17658400	Weak transcription	Adipose Nuclei	Adipose
25	chr21:17656800-17659200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:17656800-17663000	Weak transcription	Liver	Liver
27	chr21:17657000-17657800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr21:17657000-17657800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr21:17657000-17658200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr21:17657000-17659400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr21:17657400-17657800	Enhancers	Brain Hippocampus Middle	brain
32	chr21:17657400-17658000	Enhancers	Brain Anterior Caudate	brain
33	chr21:17657400-17658000	Enhancers	Fetal Brain Female	brain
34	chr21:17657600-17657800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr21:17657600-17657800	Enhancers	Brain Germinal Matrix	brain
36	chr21:17657600-17657800	Enhancers	Colon Smooth Muscle	Colon
37	chr21:17657600-17657800	Enhancers	Right Atrium	heart
38	chr21:17657600-17658200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr21:17657600-17658400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr21:17657600-17658600	Enhancers	Ovary	ovary
41	chr21:17657600-17659400	Enhancers	Duodenum Smooth Muscle	Duodenum

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