Variant report

Variant	rs28360580
Chromosome Location	chr22:31100018-31100019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11912792	1.00[ASN][1000 genomes]
rs13053290	1.00[ASN][1000 genomes]
rs13053933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13055490	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13055538	1.00[ASN][1000 genomes]
rs13056984	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433567	1.00[ASN][1000 genomes]
rs136370	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs136372	0.82[AMR][1000 genomes]
rs136373	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs136376	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs136377	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs136378	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs136381	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs136382	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs136385	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs136386	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs136390	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28672875	1.00[ASN][1000 genomes]
rs34360174	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34779325	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34944552	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34961431	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35137429	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384996	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35613453	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4820895	0.88[AMR][1000 genomes]
rs5994332	1.00[ASN][1000 genomes]
rs71331257	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7288635	1.00[ASN][1000 genomes]
rs7290980	1.00[ASN][1000 genomes]
rs9621096	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28360580	DUSP18	cis	Whole Blood	GTEx
rs28360580	CTA-963H5.5	cis	Whole Blood	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31091800-31102000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr22:31092000-31101000	Weak transcription	Gastric	stomach
3	chr22:31092200-31102200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr22:31092200-31111000	Weak transcription	Fetal Intestine Small	intestine
5	chr22:31092400-31101800	Weak transcription	Colon Smooth Muscle	Colon
6	chr22:31092400-31101800	Weak transcription	Spleen	Spleen
7	chr22:31094000-31101800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr22:31094200-31101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:31094200-31101000	Weak transcription	Brain Germinal Matrix	brain
10	chr22:31097400-31102000	Enhancers	NHDF-Ad	bronchial
11	chr22:31097600-31101800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr22:31097600-31102400	Enhancers	Brain Anterior Caudate	brain
13	chr22:31098000-31100800	Weak transcription	GM12878-XiMat	blood
14	chr22:31098200-31100800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr22:31098200-31101600	Weak transcription	Brain Hippocampus Middle	brain
16	chr22:31098200-31102000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr22:31098400-31101000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr22:31098400-31101000	Weak transcription	K562	blood
19	chr22:31098400-31101600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr22:31098400-31101600	Weak transcription	HSMM	muscle
21	chr22:31098400-31101600	Weak transcription	HSMMtube	muscle
22	chr22:31098400-31101600	Weak transcription	Osteobl	bone
23	chr22:31098400-31101800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr22:31098400-31101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:31098400-31101800	Weak transcription	NH-A	brain
26	chr22:31098400-31102000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr22:31098400-31102800	Weak transcription	NHLF	lung
28	chr22:31099000-31101600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr22:31099600-31103200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr22:31099800-31100200	Enhancers	Brain Angular Gyrus	brain
31	chr22:31099800-31100200	Enhancers	Brain Cingulate Gyrus	brain
32	chr22:31099800-31100400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr22:31099800-31101400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr22:31099800-31102000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr22:31099800-31102200	Enhancers	Fetal Brain Female	brain
36	chr22:31099800-31103800	Enhancers	Fetal Brain Male	brain
37	chr22:31100000-31100200	Genic enhancers	Brain Inferior Temporal Lobe	brain
38	chr22:31100000-31103000	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links