Variant report

Variant	rs633502
Chromosome Location	chr21:28419053-28419054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1023380	0.96[ASN][1000 genomes]
rs10432838	0.81[ASN][1000 genomes]
rs12152098	0.90[ASN][1000 genomes]
rs1391033	0.95[ASN][1000 genomes]
rs2212817	0.81[ASN][1000 genomes]
rs2830653	0.81[ASN][1000 genomes]
rs507222	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs555139	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555173	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs601784	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602794	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7280981	0.84[ASN][1000 genomes]
rs7281182	0.90[ASN][1000 genomes]

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	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2758532	chr21:28380230-28540443	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	esv2758817	chr21:28380230-28540443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	nsv587341	chr21:28391743-28419053	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs633502	APP	cis	parietal	SCAN
rs633502	ADAMTS5	cis	cerebellum	SCAN
rs633502	FAM135A	trans	parietal	SCAN
rs633502	CYYR1	cis	cerebellum	SCAN
rs633502	MRPL39	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28416800-28419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr21:28417400-28419400	Enhancers	Hela-S3	cervix
3	chr21:28417800-28420400	Weak transcription	HSMM	muscle
4	chr21:28418000-28419600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr21:28418000-28419600	Weak transcription	Psoas Muscle	Psoas
6	chr21:28418000-28419600	Weak transcription	NHDF-Ad	bronchial
7	chr21:28418200-28419600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:28418200-28419600	Weak transcription	Adipose Nuclei	Adipose
9	chr21:28418200-28419800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr21:28418400-28419200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr21:28418400-28419800	Enhancers	Ovary	ovary
12	chr21:28418800-28420600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr21:28419000-28420000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr21:28419000-28420600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:28419000-28420600	Enhancers	Colon Smooth Muscle	Colon
16	chr21:28419000-28421600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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