Variant report

Variant	rs12823372
Chromosome Location	chr12:29472216-29472217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10492383	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11608616	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609540	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610197	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610910	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11611420	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611687	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11612172	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11613628	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11614129	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11614901	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11615636	0.91[EUR][1000 genomes]
rs12809077	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12809493	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12810064	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12810315	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811201	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12811723	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12813520	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12813731	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12813789	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12813996	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12814180	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814930	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12815222	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816511	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12817163	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12817578	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12817825	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12817985	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12819896	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12821498	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12821559	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12821708	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822770	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12823422	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12823485	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823903	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12824407	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12826064	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12829666	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12830274	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12830493	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12830678	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830906	0.91[EUR][1000 genomes]
rs12831730	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12832038	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832263	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16934061	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1988943	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2350312	0.91[EUR][1000 genomes]
rs2882377	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35618989	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35636563	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36126531	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3764952	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4369447	0.83[EUR][1000 genomes]
rs67280216	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67324531	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7134744	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295387	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299158	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7299635	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7299663	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7308372	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314594	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961336	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7964254	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7979654	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][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
rs12823372	RP11-996F15.2	cis	Artery Tibial	GTEx
rs12823372	RP11-996F15.2	cis	lung	GTEx
rs12823372	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs12823372	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12823372	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs12823372	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs12823372	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12823372	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
3	chr12:29452800-29494200	Weak transcription	Lung	lung
4	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:29453800-29480000	Weak transcription	Gastric	stomach
6	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
7	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
8	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:29459600-29472800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
11	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
12	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
14	chr12:29463600-29474600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:29463800-29475400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:29464000-29476000	Weak transcription	Fetal Kidney	kidney
17	chr12:29464600-29474800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
19	chr12:29465800-29472800	Weak transcription	NHDF-Ad	bronchial
20	chr12:29466000-29474400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:29466000-29474600	Weak transcription	Placenta	Placenta
22	chr12:29466200-29472600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:29467200-29472800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:29467200-29473400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:29467200-29475800	Weak transcription	Pancreas	Pancrea
27	chr12:29467800-29474600	Weak transcription	Adipose Nuclei	Adipose
28	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:29469800-29474800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:29470000-29475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:29470000-29475200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:29470000-29475600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:29470000-29475800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:29470000-29486400	Weak transcription	Psoas Muscle	Psoas
35	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:29470000-29500000	Weak transcription	K562	blood
37	chr12:29470200-29472800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:29470200-29472800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:29470200-29473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:29470200-29475000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:29470200-29475200	Weak transcription	Primary T cells from cord blood	blood
42	chr12:29470400-29474600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:29470400-29474800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:29470600-29473000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:29470600-29473000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:29470600-29475200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:29470600-29475400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr12:29470800-29472800	Weak transcription	NH-A	brain
49	chr12:29470800-29473000	Weak transcription	Osteobl	bone
50	chr12:29470800-29474000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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