Variant report

Variant	rs11611687
Chromosome Location	chr12:29409902-29409903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10492383	0.82[EUR][1000 genomes]
rs11608616	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11609540	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11610197	0.84[EUR][1000 genomes]
rs11610910	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11611420	0.82[EUR][1000 genomes]
rs11612172	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11613628	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11614129	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11614901	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11615636	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314737	0.81[ASN][1000 genomes]
rs12809077	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12810064	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12810315	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12811723	0.84[EUR][1000 genomes]
rs12813520	0.82[EUR][1000 genomes]
rs12813789	0.86[EUR][1000 genomes]
rs12813996	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12814180	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12814930	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12815222	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12816511	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12817163	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12817578	0.85[EUR][1000 genomes]
rs12817825	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12817985	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12819896	0.84[EUR][1000 genomes]
rs12821498	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12821559	0.81[EUR][1000 genomes]
rs12821708	0.84[EUR][1000 genomes]
rs12822770	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12823372	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12823422	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12823485	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12823903	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12824407	0.84[EUR][1000 genomes]
rs12826064	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12829666	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12830274	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12830493	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12830678	0.85[EUR][1000 genomes]
rs12830906	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12831730	0.84[EUR][1000 genomes]
rs12832038	0.85[EUR][1000 genomes]
rs12832263	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16934061	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1988943	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2350312	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2882377	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34162895	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs35618989	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35636563	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36126531	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3764952	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4369447	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67280216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67324531	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134744	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7295387	0.84[EUR][1000 genomes]
rs7299158	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7299635	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7299663	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7308372	0.84[EUR][1000 genomes]
rs7314594	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7961336	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979654	0.98[AMR][1000 genomes];0.97[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11611687	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs11611687	RP11-996F15.2	cis	Thyroid	GTEx
rs11611687	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs11611687	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs11611687	RP11-996F15.2	cis	lung	GTEx
rs11611687	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11611687	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs11611687	RP11-996F15.2	cis	Artery Tibial	GTEx
rs11611687	RP11-996F15.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:19 , 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	chr12:29406400-29410000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:29408200-29413000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:29408200-29413400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:29408200-29423200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:29408200-29425800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:29408400-29414000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:29408400-29424000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:29408800-29413400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:29409200-29410000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr12:29409200-29410000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:29409200-29410000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:29409200-29412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:29409400-29410000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:29409400-29410000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:29409400-29413200	Weak transcription	Fetal Intestine Small	intestine
18	chr12:29409800-29410000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:29409800-29410000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin

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