Variant report

Variant	rs2903619
Chromosome Location	chr4:80281513-80281514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10000485	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10004440	0.95[EUR][1000 genomes]
rs10050068	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11733010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484148	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1484149	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1601201	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1601202	0.92[EUR][1000 genomes]
rs17003721	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28432328	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28516921	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28619382	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28704148	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796992	0.98[EUR][1000 genomes]
rs4975046	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975085	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818904	0.98[EUR][1000 genomes]
rs6823996	0.98[EUR][1000 genomes]
rs9992718	0.88[AMR][1000 genomes];0.98[EUR][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	nsv879505	chr4:79887043-80293046	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv999174	chr4:80212935-80512356	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3432913	chr4:80274683-80416584	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2903619	CCDC158	cis	parietal	SCAN
rs2903619	CXCL11	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80274800-80282600	Weak transcription	Fetal Brain Male	brain
2	chr4:80274800-80287000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr4:80275200-80288000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:80280800-80281800	Enhancers	Fetal Lung	lung
5	chr4:80280800-80281800	Enhancers	Rectal Smooth Muscle	rectum
6	chr4:80281200-80281600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

Quick Search:

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

what's new

Quick links