Variant report

Variant	rs249438
Chromosome Location	chr5:40806116-40806117
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs154268	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs154275	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs154280	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs154281	0.80[EUR][1000 genomes]
rs154284	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs193864	0.83[EUR][1000 genomes]
rs2008763	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs249428	0.83[EUR][1000 genomes]
rs249429	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs249437	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257009	0.83[EUR][1000 genomes]
rs29740	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs461404	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs466108	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs466962	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7711806	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs837101	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
4	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs249438	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs249438	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL
rs249438	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40800200-40808200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:40800200-40808400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:40800600-40808200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:40804000-40808200	Weak transcription	K562	blood

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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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