Variant report

Variant	rs2767499
Chromosome Location	chr1:56201024-56201025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11206663	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1165490	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1165491	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1165494	0.81[CEU][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1165495	0.81[CEU][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1165496	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1165502	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1165508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1165509	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12095642	0.82[EUR][1000 genomes]
rs2767500	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2819484	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs749330	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv829926	chr1:56188492-56360745	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	nsv546304	chr1:56195659-56240015	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2767499	PODN	cis	cerebellum	SCAN
rs2767499	FGGY	cis	cerebellum	SCAN
rs2767499	C1orf123	cis	cerebellum	SCAN
rs2767499	C1orf168	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56186400-56207600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:56193000-56206600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:56200000-56201400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:56200200-56201200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:56200200-56201400	Enhancers	NHDF-Ad	bronchial
6	chr1:56200200-56201600	Enhancers	Fetal Muscle Leg	muscle
7	chr1:56200400-56201200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:56200400-56201200	Enhancers	Osteobl	bone
9	chr1:56200600-56201200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:56200600-56201200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:56200600-56201200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:56200600-56201200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:56200600-56201400	Enhancers	HSMMtube	muscle
14	chr1:56200800-56201200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:56200800-56201400	Enhancers	HSMM	muscle
16	chr1:56201000-56206400	Weak transcription	NHLF	lung

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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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