Variant report

Variant	rs1883924
Chromosome Location	chr20:24609645-24609646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1409372	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4815280	0.84[ASW][hapmap]
rs4815281	0.84[ASW][hapmap]
rs4815284	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4815294	0.89[ASN][1000 genomes]
rs6036847	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6049799	0.92[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs6049805	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6049810	0.84[AMR][1000 genomes]
rs761437	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1883924	CST3	cis	parietal	SCAN
rs1883924	NAPB	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24584400-24612600	Weak transcription	Aorta	Aorta
2	chr20:24602400-24610000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:24607800-24611600	Enhancers	Brain Substantia Nigra	brain
4	chr20:24608200-24610000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr20:24608400-24610600	Enhancers	Spleen	Spleen
6	chr20:24608400-24611000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr20:24608400-24611000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr20:24608400-24611400	Enhancers	Fetal Heart	heart
9	chr20:24608400-24613200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:24608600-24611400	Enhancers	Fetal Thymus	thymus
11	chr20:24608600-24615000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr20:24608800-24609800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr20:24608800-24610400	Enhancers	Fetal Muscle Trunk	muscle
14	chr20:24608800-24610600	Enhancers	Primary T cells from cord blood	blood
15	chr20:24608800-24611000	Enhancers	Primary hematopoietic stem cells	blood
16	chr20:24608800-24611000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr20:24608800-24616800	Enhancers	Brain Hippocampus Middle	brain
18	chr20:24609200-24609800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr20:24609200-24610400	Enhancers	Brain Anterior Caudate	brain
20	chr20:24609200-24610600	Enhancers	Fetal Stomach	stomach
21	chr20:24609200-24610600	Enhancers	Left Ventricle	heart
22	chr20:24609200-24615200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr20:24609400-24609800	Enhancers	Duodenum Mucosa	Duodenum
24	chr20:24609400-24609800	Genic enhancers	Thymus	Thymus
25	chr20:24609400-24610400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr20:24609400-24610400	Enhancers	Right Atrium	heart
27	chr20:24609600-24610600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr20:24609600-24610600	Enhancers	Lung	lung
29	chr20:24609600-24610600	Enhancers	Right Ventricle	heart
30	chr20:24609600-24610800	Enhancers	Brain Angular Gyrus	brain
31	chr20:24609600-24612200	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links