Variant report

Variant	rs463433
Chromosome Location	chr21:28179782-28179783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs439003	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs457982	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs458027	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs458535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs458819	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs459466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461141	0.81[AFR][1000 genomes]
rs461995	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs462457	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs464293	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs464449	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs465000	0.81[AFR][1000 genomes]
rs465253	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs466551	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468725	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs468769	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1066328	chr21:28179782-28200710	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs463433	ATP5J	cis	cerebellum	SCAN
rs463433	RASEF	trans	brain	seeQTL
rs463433	AARS2	trans	brain	seeQTL
rs463433	VANGL1	trans	cerebellum	SCAN
rs463433	NANS	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28170800-28181000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr21:28174000-28185400	Weak transcription	HSMMtube	muscle
3	chr21:28174600-28187800	Weak transcription	Osteobl	bone
4	chr21:28177800-28186800	Weak transcription	NHLF	lung
5	chr21:28178200-28183000	Weak transcription	Fetal Stomach	stomach
6	chr21:28178200-28185800	Weak transcription	Ovary	ovary
7	chr21:28178800-28179800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:28178800-28179800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr21:28178800-28179800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr21:28178800-28179800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr21:28178800-28179800	Enhancers	HMEC	breast
12	chr21:28178800-28179800	Enhancers	NHEK	skin
13	chr21:28178800-28180000	Enhancers	Hela-S3	cervix
14	chr21:28178800-28180200	Enhancers	Dnd41	blood
15	chr21:28179200-28179800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:28179200-28183200	Weak transcription	NHDF-Ad	bronchial
17	chr21:28179400-28180000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:28179400-28183000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr21:28179400-28183400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

Quick Search:

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

what's new

Quick links