Variant report

Variant	rs2370982
Chromosome Location	chr14:79890677-79890678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10136360	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10145154	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10146690	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10146997	0.91[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10150332	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10150482	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11625620	0.81[LWK][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs11625769	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs17109221	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17109256	0.91[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17836088	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7144011	0.91[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7154797	0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs7156625	0.91[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72690737	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8008910	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8020365	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931412	chr14:79420297-79928269	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv902110	chr14:79624492-79998294	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv530072	chr14:79769657-79928269	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv902111	chr14:79807197-79890677	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1045241	chr14:79885361-80734201	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2370982	NRXN3	cis	cerebellum	SCAN
rs2370982	C14orf179	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79881200-79896000	Weak transcription	Aorta	Aorta
2	chr14:79884200-79901800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr14:79886200-79892000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:79887000-79892000	Weak transcription	Fetal Intestine Large	intestine
5	chr14:79887000-79892200	Weak transcription	Liver	Liver
6	chr14:79888000-79893000	Weak transcription	Fetal Intestine Small	intestine

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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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