Variant report

Variant	rs11180460
Chromosome Location	chr12:75716278-75716279
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:75716206-75716630	IMR90	lung:	n/a	chr12:75716474-75716487 chr12:75716228-75716241

Variant related genes	Relation type
CAPS2	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10506668	0.95[MEX][hapmap]
rs1051446	0.81[MEX][hapmap]
rs10879900	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10879902	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10879903	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10879922	0.95[MEX][hapmap]
rs11180456	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes]
rs11180458	0.82[EUR][1000 genomes]
rs11180465	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180470	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs11180473	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs11180474	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11180475	0.84[AMR][1000 genomes]
rs11180483	0.85[MEX][hapmap]
rs11180540	0.90[MEX][hapmap]
rs11180548	0.95[MEX][hapmap]
rs11610111	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11610112	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11831200	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11837697	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366348	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs12367329	0.85[AMR][1000 genomes]
rs12368429	0.87[AMR][1000 genomes]
rs12369556	0.86[MEX][hapmap]
rs12369854	0.81[EUR][1000 genomes]
rs12372516	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs12581394	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12581416	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1909979	0.90[MEX][hapmap]
rs2242435	0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs3087687	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741496	0.81[MEX][hapmap]
rs4394867	0.95[MEX][hapmap]
rs4565940	0.95[MEX][hapmap]
rs4623941	0.85[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs4882616	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882618	0.90[MEX][hapmap]
rs4882687	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4882689	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs60971359	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7136911	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7297994	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap]
rs7298343	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs73364090	0.85[AMR][1000 genomes]
rs73364096	0.85[AMR][1000 genomes]
rs7954879	0.89[CEU][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7967619	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7969930	0.90[MEX][hapmap]
rs7970188	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7974011	0.90[MEX][hapmap]
rs7975661	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs7978312	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]

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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11180460	GLIPR1L2	cis	Artery Tibial	GTEx
rs11180460	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs11180460	GLIPR1L2	cis	parietal	SCAN
rs11180460	GLIPR1	cis	Whole Blood	GTEx
rs11180460	GLIPR1L2	cis	Nerve Tibial	GTEx
rs11180460	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs11180460	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs11180460	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs11180460	GLIPR1L2	cis	Stomach	GTEx
rs11180460	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs11180460	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs11180460	GLIPR1L2	cis	lung	GTEx
rs11180460	GLIPR1L2	cis	cerebellum	SCAN
rs11180460	RP11-585P4.5	cis	Thyroid	GTEx
rs11180460	RP11-585P4.5	cis	Artery Tibial	GTEx
rs11180460	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs11180460	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs11180460	GLIPR1L2	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75700000-75723000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:75700000-75723400	Weak transcription	Ovary	ovary
3	chr12:75706200-75723400	Weak transcription	Left Ventricle	heart
4	chr12:75709400-75723600	Weak transcription	HSMMtube	muscle
5	chr12:75716000-75716400	Enhancers	A549	lung
6	chr12:75716000-75716400	Flanking Active TSS	NHDF-Ad	bronchial
7	chr12:75716000-75716600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:75716000-75716600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:75716200-75716400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:75716200-75716400	Flanking Active TSS	Osteobl	bone

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