Variant report

Variant	rs2420378
Chromosome Location	chr1:169569918-169569919
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1997664	0.90[ASN][1000 genomes]
rs2142760	0.90[ASN][1000 genomes]
rs2205895	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2205896	0.84[ASN][1000 genomes]
rs2223303	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298903	0.88[AFR][1000 genomes]
rs3766126	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3917750	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3917751	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3917768	0.90[ASN][1000 genomes]
rs3917775	0.90[ASN][1000 genomes]
rs3917777	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3917782	0.84[ASN][1000 genomes]
rs3917783	0.84[ASN][1000 genomes]
rs3917786	0.84[ASN][1000 genomes]
rs6127	0.84[ASN][1000 genomes]
rs742127	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs760694	0.93[ASN][1000 genomes]

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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872538	chr1:169567516-169576207	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv2762197	chr1:169568646-169572345	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2420378	METTL13	cis	parietal	SCAN
rs2420378	ATP1B1	cis	cerebellum	SCAN
rs2420378	F5	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169558800-169570000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:169559200-169570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:169564000-169570200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:169565200-169570400	Weak transcription	GM12878-XiMat	blood
5	chr1:169565400-169581400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:169569800-169570600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:169569800-169576400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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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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