Variant report

Variant	rs12368429
Chromosome Location	chr12:75725636-75725637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10879900	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180456	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180458	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180460	0.87[AMR][1000 genomes]
rs11180465	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180473	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180475	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11520223	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610111	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11610112	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11837697	0.84[AMR][1000 genomes]
rs12366348	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12367329	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12369556	0.80[EUR][1000 genomes]
rs12369854	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12371293	0.80[EUR][1000 genomes]
rs12372516	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581394	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087687	0.81[AMR][1000 genomes]
rs3923914	0.80[EUR][1000 genomes]
rs4623941	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882616	0.84[AMR][1000 genomes]
rs4882618	0.80[EUR][1000 genomes]
rs4882687	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882689	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60971359	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136911	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73191008	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73364090	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73364096	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954879	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967619	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7970188	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975661	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv520424	chr12:75646788-75740883	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv526556	chr12:75653281-75740883	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1054059	chr12:75654631-75776721	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv899312	chr12:75692261-75790817	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs12368429	RP11-585P4.5	cis	Thyroid	GTEx
rs12368429	GLIPR1L2	cis	Artery Tibial	GTEx
rs12368429	GLIPR1L2	cis	lung	GTEx
rs12368429	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs12368429	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs12368429	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12368429	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs12368429	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs12368429	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs12368429	RP11-585P4.5	cis	Artery Tibial	GTEx
rs12368429	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs12368429	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs12368429	GLIPR1L2	cis	Stomach	GTEx
rs12368429	GLIPR1L2	cis	Nerve Tibial	GTEx
rs12368429	GLIPR1L2	cis	Thyroid	GTEx
rs12368429	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs12368429	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs12368429	GLIPR1L2	cis	Artery Aorta	GTEx
rs12368429	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs12368429	GLIPR1L2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75724000-75728000	Weak transcription	Stomach Mucosa	stomach
2	chr12:75724000-75728000	Weak transcription	Spleen	Spleen
3	chr12:75724000-75728400	Weak transcription	Fetal Heart	heart
4	chr12:75724200-75728000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:75724200-75728000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:75724200-75728000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:75724200-75728000	Weak transcription	Placenta	Placenta
8	chr12:75724200-75728000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:75724200-75728000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:75724200-75728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:75724200-75728200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:75724200-75728200	Weak transcription	Lung	lung
13	chr12:75724200-75728200	Weak transcription	Pancreas	Pancrea
14	chr12:75724200-75728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:75724200-75728400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:75724200-75728400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:75724400-75727600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:75724400-75727600	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:75724400-75727600	Weak transcription	NHLF	lung
20	chr12:75724400-75727800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:75724400-75727800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:75724400-75727800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:75724400-75728000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:75724400-75728000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:75724400-75728000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:75724400-75728000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:75724400-75728000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:75724400-75728000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:75724400-75728000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:75724400-75728000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:75724400-75728000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:75724400-75728000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:75724400-75728000	Weak transcription	Adipose Nuclei	Adipose
34	chr12:75724400-75728000	Weak transcription	Brain Angular Gyrus	brain
35	chr12:75724400-75728000	Weak transcription	Brain Germinal Matrix	brain
36	chr12:75724400-75728000	Weak transcription	Fetal Kidney	kidney
37	chr12:75724400-75728000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:75724400-75728000	Weak transcription	Fetal Thymus	thymus
39	chr12:75724400-75728000	Weak transcription	Right Atrium	heart
40	chr12:75724400-75728000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:75724400-75728000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:75724400-75728000	Weak transcription	HMEC	breast
43	chr12:75724400-75728000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:75724400-75728000	Weak transcription	NH-A	brain
45	chr12:75724400-75728000	Weak transcription	NHDF-Ad	bronchial
46	chr12:75724400-75728000	Weak transcription	Osteobl	bone
47	chr12:75724400-75728200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:75724400-75728200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:75724400-75728200	Weak transcription	HUVEC	blood vessel
50	chr12:75724400-75728400	Weak transcription	H1 Cell Line	embryonic stem cell

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