Variant report

Variant	rs2280322
Chromosome Location	chr4:166428294-166428295
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1530044	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17046550	0.93[ASN][1000 genomes]
rs2280323	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280324	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691201	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58288308	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60132258	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6828294	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6846466	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666366	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7677837	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677998	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7692951	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7697955	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv508327	chr4:166424440-166475679	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280322	TKTL2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166420800-166433400	Weak transcription	Brain Germinal Matrix	brain
2	chr4:166421000-166428800	Weak transcription	Brain Anterior Caudate	brain
3	chr4:166421400-166433200	Weak transcription	Fetal Brain Male	brain
4	chr4:166421800-166428400	Weak transcription	Aorta	Aorta
5	chr4:166421800-166428800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:166422000-166433200	Weak transcription	Fetal Brain Female	brain
7	chr4:166423200-166428600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:166425200-166428400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:166426400-166428600	Enhancers	Rectal Smooth Muscle	rectum
10	chr4:166427000-166428400	Enhancers	Adipose Nuclei	Adipose
11	chr4:166427000-166428400	Enhancers	Fetal Heart	heart
12	chr4:166427000-166428400	Enhancers	Fetal Lung	lung
13	chr4:166427000-166428400	Enhancers	NHEK	skin
14	chr4:166427000-166428600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:166427000-166428600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:166427000-166428600	Enhancers	Osteobl	bone
17	chr4:166427000-166428800	Enhancers	Colon Smooth Muscle	Colon
18	chr4:166427000-166429200	Enhancers	Fetal Stomach	stomach
19	chr4:166427000-166429800	Enhancers	Hela-S3	cervix
20	chr4:166427000-166429800	Enhancers	HepG2	liver
21	chr4:166427000-166429800	Enhancers	NHLF	lung
22	chr4:166427600-166428400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:166427800-166428400	Enhancers	Esophagus	oesophagus
24	chr4:166428000-166429000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:166428200-166428400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:166428200-166428400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:166428200-166428400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:166428200-166428400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:166428200-166428400	Enhancers	Brain Substantia Nigra	brain
30	chr4:166428200-166428600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:166428200-166428600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr4:166428200-166428800	Enhancers	Cortex derived primary cultured neurospheres	brain

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