Variant report

Variant	rs12366348
Chromosome Location	chr12:75760742-75760743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLIPR1L2-2	chr12:75760613-75760793	NONHSAT029533

Extended variants
information (count: 79 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10506668	0.86[JPT][hapmap]
rs10785187	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10879900	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879902	0.87[CHB][hapmap]
rs10879903	0.87[CHB][hapmap]
rs10879905	0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10879906	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10879907	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10879922	0.82[JPT][hapmap]
rs11180455	0.81[JPT][hapmap]
rs11180456	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11180458	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180460	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs11180465	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180470	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11180473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180474	0.87[CHB][hapmap]
rs11180475	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180483	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180484	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180488	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11180489	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180492	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11180512	0.82[JPT][hapmap]
rs11180540	0.82[JPT][hapmap]
rs11180548	0.82[JPT][hapmap]
rs11520223	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11610111	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11610112	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11831200	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs11837697	0.83[AMR][1000 genomes]
rs12367329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12368429	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12369556	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12369854	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12371293	0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12372516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581394	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12581416	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs1909979	0.82[JPT][hapmap]
rs3087687	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes]
rs3923914	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4394867	0.86[JPT][hapmap]
rs4409878	0.82[JPT][hapmap]
rs4415811	0.83[JPT][hapmap]
rs4565940	0.86[JPT][hapmap]
rs4583012	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4623941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882616	0.86[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4882618	0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4882619	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4882620	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4882687	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60971359	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67904412	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7135440	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7136911	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297994	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs7298343	0.81[CEU][hapmap]
rs73191008	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73364090	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73364096	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73365996	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7954879	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967619	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969930	0.82[JPT][hapmap]
rs7970188	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970458	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7974011	0.82[JPT][hapmap]
rs7975661	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7978312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7978856	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs12366348	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs12366348	GLIPR1L2	cis	Thyroid	GTEx
rs12366348	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs12366348	RP11-585P4.5	cis	Thyroid	GTEx
rs12366348	GLIPR1L2	cis	Artery Tibial	GTEx
rs12366348	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs12366348	GLIPR1L2	cis	lung	GTEx
rs12366348	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs12366348	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs12366348	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs12366348	GLIPR1L2	cis	Stomach	GTEx
rs12366348	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs12366348	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs12366348	GLIPR1L1	cis	multi-tissue	Pritchard
rs12366348	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs12366348	RP11-585P4.5	cis	Artery Tibial	GTEx
rs12366348	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs12366348	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs12366348	GLIPR1L2	cis	Artery Aorta	GTEx
rs12366348	GLIPR1L2	cis	Nerve Tibial	GTEx
rs12366348	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75749600-75782800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:75749800-75771800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:75754000-75784200	Weak transcription	Right Ventricle	heart
4	chr12:75757200-75783400	Weak transcription	Ovary	ovary
5	chr12:75758200-75782600	Weak transcription	Aorta	Aorta
6	chr12:75758600-75760800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:75758600-75760800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:75759800-75760800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:75759800-75760800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:75759800-75760800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:75759800-75761000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:75760000-75760800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:75760000-75760800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:75760000-75760800	Enhancers	NH-A	brain
15	chr12:75760000-75761000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:75760000-75761200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:75760200-75760800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr12:75760200-75760800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:75760200-75760800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:75760200-75760800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr12:75760200-75760800	Enhancers	HSMM	muscle
22	chr12:75760200-75760800	Enhancers	HUVEC	blood vessel
23	chr12:75760200-75760800	Enhancers	NHDF-Ad	bronchial
24	chr12:75760200-75760800	Enhancers	NHLF	lung
25	chr12:75760200-75761000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr12:75760200-75761000	Enhancers	GM12878-XiMat	blood
27	chr12:75760200-75761000	Enhancers	Osteobl	bone
28	chr12:75760200-75761600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr12:75760400-75760800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:75760400-75760800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:75760400-75760800	Enhancers	NHEK	skin
32	chr12:75760400-75761000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:75760400-75763400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr12:75760600-75760800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:75760600-75760800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:75760600-75761000	Active TSS	H9 Cell Line	embryonic stem cell
37	chr12:75760600-75761000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr12:75760600-75761000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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