Variant report

Variant	rs1419090
Chromosome Location	chr1:211641950-211641951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11577985	0.85[CHD][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap]
rs11581989	0.85[CHD][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap]
rs11582143	0.86[ASW][hapmap];0.85[CHD][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.89[YRI][hapmap]
rs17017361	0.80[LWK][hapmap]
rs17017394	0.85[CHD][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap]
rs17017399	0.85[CHD][hapmap];0.80[LWK][hapmap];0.89[MEX][hapmap]
rs17017431	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17017432	0.86[ASW][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs17017441	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17017451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6666324	0.89[YRI][hapmap]
rs6699139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7529673	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7533617	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7536058	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7538100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547352	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][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	nsv832514	chr1:211630247-211794963	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1419090	CTSE	cis	parietal	SCAN
rs1419090	LINC00467	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211641000-211643400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:211641000-211643800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:211641000-211644000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:211641000-211644000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:211641200-211643200	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:211641400-211642200	Enhancers	Brain Hippocampus Middle	brain
7	chr1:211641400-211643800	Enhancers	HUVEC	blood vessel
8	chr1:211641800-211642000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:211641800-211642200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:211641800-211642800	Weak transcription	Adipose Nuclei	Adipose

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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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