Variant report

Variant	rs3004153
Chromosome Location	chr20:23642458-23642459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1884861	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424590	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2424591	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2424598	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004154	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3341096	chr20:23638652-23642850	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv458950	chr20:23642427-23721992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv585724	chr20:23642427-23721992	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3004153	CST3	cis	cerebellum	SCAN
rs3004153	CST3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23637200-23643600	Weak transcription	Right Atrium	heart
2	chr20:23637200-23660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23637800-23644200	Enhancers	Fetal Intestine Large	intestine
4	chr20:23638400-23644200	Enhancers	Fetal Intestine Small	intestine
5	chr20:23639400-23643200	Flanking Active TSS	HepG2	liver
6	chr20:23639800-23643400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:23640000-23642600	Enhancers	Duodenum Mucosa	Duodenum
8	chr20:23641200-23643000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr20:23641400-23642600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr20:23641800-23643000	Weak transcription	Fetal Muscle Leg	muscle
11	chr20:23641800-23647000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr20:23641800-23647200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:23641800-23647200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:23641800-23652200	Weak transcription	Adipose Nuclei	Adipose
15	chr20:23642000-23642600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr20:23642200-23642600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr20:23642200-23642600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr20:23642400-23644800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:23642400-23649400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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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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