Variant report

Variant	rs242109
Chromosome Location	chr14:69458252-69458253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10151419	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11623192	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1275194	0.91[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs1983700	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2012752	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs242091	0.82[EUR][1000 genomes]
rs242097	0.91[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs242100	0.82[MEX][hapmap]
rs242101	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs242102	0.91[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs242104	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28396849	0.81[ASN][1000 genomes]
rs28698682	0.81[ASN][1000 genomes]
rs436106	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4899275	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4902683	0.95[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7140693	1.00[JPT][hapmap]
rs761898	0.82[MEX][hapmap]
rs927064	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.86[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	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs242109	GALNTL1	cis	cerebellum	SCAN
rs242109	MAP3K9	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69447000-69471400	Weak transcription	Esophagus	oesophagus
2	chr14:69449200-69458400	Weak transcription	HUVEC	blood vessel
3	chr14:69453400-69460600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr14:69454800-69461200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr14:69455600-69465200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:69456000-69464400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:69456000-69471200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:69458200-69459000	Enhancers	Spleen	Spleen

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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