Variant report

Variant	rs7354930
Chromosome Location	chr1:66986377-66986378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10889624	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10889625	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11208903	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12143964	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1338184	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1338194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1338200	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1415974	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1415984	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1547737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1856315	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1947083	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2121051	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2859914	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4142763	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4655494	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6588203	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6588204	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691033	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7354983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355221	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7540195	0.81[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7543607	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs967322	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs967325	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs984409	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs994396	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][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	nsv518465	chr1:66986377-66988586	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7354930	TCTEX1D1	cis	cerebellum	SCAN
rs7354930	TCTEX1D1	cis	parietal	SCAN
rs7354930	SGIP1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:66983600-66987200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:66985800-66988000	Enhancers	A549	lung
3	chr1:66986000-66987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:66986000-66987200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:66986000-66987200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:66986200-66986400	Enhancers	Osteobl	bone
7	chr1:66986200-66989400	Weak transcription	HepG2	liver

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