Variant report

Variant	rs11168187
Chromosome Location	chr12:48044011-48044012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10875683	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11168170	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168177	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168194	0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs11830795	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11834770	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12229373	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1235152	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12422983	0.83[CEU][hapmap]
rs12426774	0.85[CEU][hapmap]
rs12809264	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12810487	0.85[CEU][hapmap]
rs12812460	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12812960	0.81[ASN][1000 genomes]
rs12818241	0.85[CEU][hapmap]
rs12819759	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12820269	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074531	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2074532	0.86[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2077621	0.83[ASN][1000 genomes]
rs2238144	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2239188	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2283345	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2285830	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs3764015	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3764016	0.85[ASN][1000 genomes]
rs3764018	0.86[ASN][1000 genomes]
rs3764019	0.86[ASN][1000 genomes]
rs3764020	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs4505143	0.82[ASN][1000 genomes]
rs4537844	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6580635	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6580636	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs71445738	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs726588	0.82[ASN][1000 genomes]
rs7302276	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7306556	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs757284	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7967336	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7967546	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs7976708	0.86[ASN][1000 genomes]
rs867143	0.83[ASN][1000 genomes]
rs972688	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv558786	chr12:47942029-48044011	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv527728	chr12:47954597-48044506	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv521329	chr12:48044011-48051456	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Vertical cup-disc ratio	25241763	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11168187	RAPGEF3	cis	cerebellum	SCAN
rs11168187	TMEM117	cis	cerebellum	SCAN
rs11168187	RAPGEF3	cis	parietal	SCAN
rs11168187	PUS7L	cis	parietal	SCAN
rs11168187	PRICKLE1	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48007400-48044800	Weak transcription	Aorta	Aorta
2	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:48015600-48055200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:48016000-48044400	Weak transcription	NH-A	brain
5	chr12:48023600-48044800	Weak transcription	Gastric	stomach
6	chr12:48029400-48055400	Weak transcription	Thymus	Thymus
7	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:48031000-48044600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48031000-48083200	Weak transcription	Esophagus	oesophagus
10	chr12:48031200-48051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:48031200-48053200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:48031400-48044600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:48031400-48046200	Weak transcription	Fetal Stomach	stomach
14	chr12:48031400-48058400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:48031600-48044600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:48032200-48045800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:48035000-48044600	Weak transcription	HSMM	muscle
18	chr12:48036400-48044600	Weak transcription	NHDF-Ad	bronchial
19	chr12:48036600-48055400	Weak transcription	Ovary	ovary
20	chr12:48038200-48044200	Weak transcription	Osteobl	bone
21	chr12:48038200-48059400	Weak transcription	Small Intestine	intestine
22	chr12:48038400-48044200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:48038600-48051400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:48038800-48044600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:48038800-48045000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:48038800-48045800	Weak transcription	Primary T cells from cord blood	blood
27	chr12:48038800-48046000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:48039000-48044600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:48039000-48052800	Weak transcription	Dnd41	blood
30	chr12:48039200-48044600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:48039200-48044800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:48039200-48045000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:48039200-48046000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:48039200-48046200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:48039200-48052800	Weak transcription	Fetal Intestine Large	intestine
36	chr12:48039400-48045000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:48039400-48058400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:48039800-48045400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:48040000-48044200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:48040000-48051400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:48040200-48044200	Weak transcription	GM12878-XiMat	blood
42	chr12:48040200-48045600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:48040200-48050000	Weak transcription	Primary B cells from cord blood	blood
44	chr12:48040400-48044800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:48040600-48045600	Weak transcription	Fetal Kidney	kidney
46	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
47	chr12:48040800-48045000	Weak transcription	HMEC	breast
48	chr12:48041400-48045000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:48041800-48044200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:48042200-48044200	Weak transcription	A549	lung

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