Variant report

Variant	rs11181483
Chromosome Location	chr12:42798384-42798385
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1051453	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880283	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880294	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11181398	0.80[EUR][1000 genomes]
rs11181399	0.80[EUR][1000 genomes]
rs11181422	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181433	0.84[AFR][1000 genomes]
rs11181454	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181463	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11181465	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181466	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181467	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181499	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181501	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181502	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181507	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12228205	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12308219	0.80[EUR][1000 genomes]
rs12366848	0.83[EUR][1000 genomes]
rs12371762	0.83[EUR][1000 genomes]
rs12423048	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12815283	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12820154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551210	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669886	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669892	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669893	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669904	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669907	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1669910	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669936	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17551006	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796380	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796381	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796382	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796384	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796386	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796388	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1796394	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1839935	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2178753	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2406674	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2406875	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2600908	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708058	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708059	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3747558	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3747560	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3810793	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4359266	0.81[EUR][1000 genomes]
rs4768399	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768402	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768411	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768413	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55702525	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56051354	0.88[ASN][1000 genomes]
rs56290913	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61926593	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582395	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6582398	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7133836	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71453350	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7296357	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7305397	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307790	0.83[ASN][1000 genomes]
rs7959338	0.90[ASN][1000 genomes]
rs7965743	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969910	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7970003	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11181483	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs11181483	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
3	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:42721800-42803600	Weak transcription	Gastric	stomach
5	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:42763800-42804200	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:42767200-42836200	Weak transcription	Esophagus	oesophagus
8	chr12:42770200-42815800	Weak transcription	Fetal Lung	lung
9	chr12:42770400-42816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:42771000-42799000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:42771200-42801000	Weak transcription	NH-A	brain
12	chr12:42771800-42803000	Weak transcription	Brain Anterior Caudate	brain
13	chr12:42777000-42802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:42779000-42798400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:42780200-42802800	Weak transcription	Right Ventricle	heart
16	chr12:42780200-42836000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:42780400-42804200	Weak transcription	K562	blood
18	chr12:42780400-42811200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:42782000-42802000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:42782800-42803400	Weak transcription	Spleen	Spleen
21	chr12:42782800-42804200	Weak transcription	Fetal Brain Female	brain
22	chr12:42782800-42807200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:42783000-42836000	Weak transcription	Lung	lung
24	chr12:42785400-42836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:42789600-42812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:42789600-42836200	Weak transcription	Pancreas	Pancrea
27	chr12:42790600-42802600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:42790600-42803800	Weak transcription	Colonic Mucosa	Colon
29	chr12:42792000-42799200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:42792000-42800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:42792200-42799800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:42793200-42802200	Weak transcription	Brain Angular Gyrus	brain
33	chr12:42793200-42806800	Weak transcription	Brain Substantia Nigra	brain
34	chr12:42793800-42801000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:42793800-42802600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:42793800-42803400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:42793800-42840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:42794000-42802400	Weak transcription	HUVEC	blood vessel
39	chr12:42794400-42803800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:42794800-42804200	Weak transcription	Fetal Kidney	kidney
41	chr12:42795000-42813600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:42795400-42800600	Weak transcription	HMEC	breast
43	chr12:42795400-42804000	Weak transcription	Placenta	Placenta
44	chr12:42795400-42834600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:42795600-42799200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:42795600-42799800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:42795600-42800800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr12:42795600-42806000	Weak transcription	Primary T cells from cord blood	blood
49	chr12:42795600-42811400	Weak transcription	Adipose Nuclei	Adipose
50	chr12:42795600-42811800	Weak transcription	Rectal Mucosa Donor 29	rectum

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