Variant report

Variant	rs12023399
Chromosome Location	chr1:216819427-216819428
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10863260	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11117634	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11117635	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1414529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1419244	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]
rs1857412	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1857413	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4846609	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12023399	PIK3CG	trans	parietal	SCAN
rs12023399	TGFB2	cis	parietal	SCAN
rs12023399	ATF3	cis	cerebellum	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	chr1:216800000-216826200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:216800200-216826600	Weak transcription	Left Ventricle	heart
5	chr1:216814000-216856200	Weak transcription	Psoas Muscle	Psoas
6	chr1:216815800-216819800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:216816000-216819800	Weak transcription	Fetal Heart	heart
8	chr1:216818600-216835000	Weak transcription	Fetal Intestine Large	intestine

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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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