Variant report

Variant	rs6049825
Chromosome Location	chr20:24618695-24618696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1997870	0.91[JPT][hapmap]
rs4813522	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes]
rs6076239	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs6132754	0.88[JPT][hapmap]

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	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
3	nsv912824	chr20:24612808-24639916	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6049825	CST3	cis	parietal	SCAN
rs6049825	C20orf3	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24614000-24619400	Weak transcription	Gastric	stomach
2	chr20:24614200-24619200	Weak transcription	Aorta	Aorta
3	chr20:24614600-24619800	Weak transcription	Esophagus	oesophagus
4	chr20:24615200-24620200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:24615400-24633800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr20:24615600-24619400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:24616200-24619000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr20:24616200-24619600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:24616200-24639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:24616400-24630200	Weak transcription	Brain Angular Gyrus	brain
11	chr20:24616600-24619400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:24616800-24619200	Weak transcription	Brain Hippocampus Middle	brain
13	chr20:24617200-24618800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:24617800-24623600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr20:24618200-24619600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr20:24618200-24619800	Enhancers	Brain Substantia Nigra	brain
17	chr20:24618200-24620200	Enhancers	Thymus	Thymus
18	chr20:24618400-24621000	Enhancers	Fetal Thymus	thymus
19	chr20:24618600-24618800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr20:24618600-24619000	Weak transcription	A549	lung
21	chr20:24618600-24620000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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