Variant report

Variant	rs36040692
Chromosome Location	chr12:29389131-29389132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11609540	0.81[AFR][1000 genomes]
rs11610910	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11612172	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11614129	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11614901	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12809077	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12817825	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12822770	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12826064	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12830274	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12830493	0.81[AFR][1000 genomes]
rs16934061	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4369447	0.80[EUR][1000 genomes]
rs67324531	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7299158	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7299635	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7299663	0.86[AFR][1000 genomes];0.88[AMR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs36040692	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs36040692	RP11-996F15.2	cis	lung	GTEx
rs36040692	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs36040692	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs36040692	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs36040692	RP11-996F15.2	cis	Thyroid	GTEx
rs36040692	RP11-996F15.2	cis	Artery Tibial	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29366200-29393200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:29379000-29393400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:29379600-29394600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:29380400-29392000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:29381000-29393200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:29381800-29394600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:29381800-29394800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:29382000-29390000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:29382200-29393400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:29383200-29391600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:29383400-29392000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:29384000-29393200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:29384400-29393200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:29387800-29391800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:29388400-29390200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:29388400-29391800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:29388600-29391800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:29388600-29392000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:29388600-29394800	Weak transcription	NHEK	skin
20	chr12:29388800-29391800	Weak transcription	NH-A	brain
21	chr12:29388800-29394600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:29389000-29390200	Weak transcription	HUVEC	blood vessel

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