Variant report

Variant	rs1419244
Chromosome Location	chr1:216802941-216802942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10863260	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11117634	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11117635	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12023399	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1414529	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1846228	0.87[JPT][hapmap]
rs1857412	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1857413	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4846609	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873178	chr1:216714314-216813244	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1419244	ATF3	cis	cerebellum	SCAN
rs1419244	PIK3CG	trans	parietal	SCAN
rs1419244	TGFB2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216775200-216835400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:216787400-216853800	Weak transcription	Pancreas	Pancrea
3	chr1:216792400-216809000	Weak transcription	Gastric	stomach
4	chr1:216800000-216806600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:216800000-216826200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:216800200-216826600	Weak transcription	Left Ventricle	heart
7	chr1:216801400-216803200	Weak transcription	Fetal Heart	heart
8	chr1:216802800-216803200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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Input of quick search could be:

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

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