Variant report

Variant	rs249437
Chromosome Location	chr5:40809100-40809101
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1070446	0.92[ASN][1000 genomes]
rs1097546	0.82[ASN][1000 genomes]
rs154268	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs154275	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs154280	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs154281	0.90[EUR][1000 genomes]
rs154284	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171605	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171606	0.86[EUR][1000 genomes]
rs173620	0.92[ASN][1000 genomes]
rs192219	0.92[ASN][1000 genomes]
rs193864	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2008763	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2161521	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249420	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs249422	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249423	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249425	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249428	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249429	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249438	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs249441	0.98[ASN][1000 genomes]
rs257009	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs29740	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs29742	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs29743	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs29744	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs29761	0.92[ASN][1000 genomes]
rs376831	0.82[ASN][1000 genomes]
rs381471	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs389737	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs432071	0.82[ASN][1000 genomes]
rs453037	0.82[ASN][1000 genomes]
rs457776	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs461404	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs462366	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs466108	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs466962	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6897470	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7711806	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs837101	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][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
rs249437	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL
rs249437	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs249437	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40807800-40809800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:40808200-40809200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:40808200-40809200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:40808200-40809200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:40808200-40809200	Enhancers	A549	lung
6	chr5:40808200-40809200	Enhancers	K562	blood
7	chr5:40808200-40809200	Enhancers	NH-A	brain
8	chr5:40808200-40809200	Enhancers	NHLF	lung
9	chr5:40808200-40809200	Enhancers	Osteobl	bone
10	chr5:40808400-40809200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:40808400-40809200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:40808400-40809200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:40808400-40809200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:40808400-40809200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:40808400-40809200	Enhancers	NHDF-Ad	bronchial
16	chr5:40808400-40826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:40808600-40809200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:40808600-40814000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:40808800-40825600	Weak transcription	HSMM	muscle
20	chr5:40809000-40813800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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