Variant report

Variant	rs2819513
Chromosome Location	chr1:227630987-227630988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10916145	0.84[ASW][hapmap];0.85[CHD][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs11799974	0.85[CHD][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs11802190	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493824	0.88[CHD][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs2644136	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2644141	0.83[AFR][1000 genomes]
rs2814087	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814091	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2819515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819516	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2819519	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7546172	0.85[CHD][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2819513	CDC42BPA	cis	lymphoblastoid	seeQTL
rs2819513	ITPKB	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227617600-227631200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:227625600-227631600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:227625600-227632000	Weak transcription	Fetal Kidney	kidney
4	chr1:227628800-227631800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:227629000-227631600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:227629000-227631800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:227629000-227632000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:227629000-227635200	Weak transcription	HUVEC	blood vessel
9	chr1:227629200-227631600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:227630000-227631200	Weak transcription	Right Atrium	heart
11	chr1:227630000-227634800	Weak transcription	Left Ventricle	heart
12	chr1:227630000-227636600	Weak transcription	Right Ventricle	heart
13	chr1:227630400-227632000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:227630600-227632600	Enhancers	Brain Angular Gyrus	brain

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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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