Variant report

Variant	rs12809077
Chromosome Location	chr12:29403492-29403493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11608616	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11609540	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11610910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11611687	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11612172	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11613628	0.84[EUR][1000 genomes]
rs11614129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11614901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11615636	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12810064	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12810315	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12813996	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12814180	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12814930	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12815222	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12816511	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817163	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817825	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12817985	0.90[EUR][1000 genomes]
rs12821498	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12822770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823372	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12823422	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823485	0.84[EUR][1000 genomes]
rs12823903	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12826064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829666	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12830274	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12830493	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12830906	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12832263	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16934061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1988943	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2350312	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882377	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34162895	0.80[AMR][1000 genomes]
rs35618989	0.81[AMR][1000 genomes]
rs35636563	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36040692	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36126531	0.80[AMR][1000 genomes]
rs4369447	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67280216	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67324531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134744	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7299158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299635	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7314594	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7961336	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7964254	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979654	0.80[AMR][1000 genomes];0.89[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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12809077	RP11-996F15.2	cis	Artery Tibial	GTEx
rs12809077	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12809077	RP11-996F15.2	cis	lung	GTEx
rs12809077	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs12809077	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12809077	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs12809077	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs12809077	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29396800-29413200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:29400800-29411400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:29402000-29408000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:29402600-29404600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:29402800-29404000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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