Variant report

Variant	rs10459290
Chromosome Location	chr12:42613290-42613291
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42612206..42614346-chr12:42630499..42633033,4	MCF-7	breast:
2	chr12:42605935..42607831-chr12:42611202..42613567,2	K562	blood:
3	chr12:42600600..42602301-chr12:42611820..42613323,2	K562	blood:
4	chr12:42610242..42612144-chr12:42612855..42615684,2	K562	blood:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10492388	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059360	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785333	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10785334	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880256	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880258	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880259	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880260	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880261	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10880264	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880268	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880269	0.83[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880272	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880273	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181328	0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs11181364	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181378	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11181380	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181398	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181399	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181422	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs11181463	0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs12049942	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12308219	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12366848	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12370778	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12371615	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12371762	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12372623	0.87[AFR][1000 genomes]
rs1669892	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs1796384	0.80[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs2178753	0.81[CHB][hapmap]
rs2406567	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2406568	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2406674	0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs3229	0.91[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap]
rs3747557	0.80[CHB][hapmap]
rs3747560	0.81[CHB][hapmap]
rs3810793	0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs6582390	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582391	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7138877	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7312933	0.91[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs7315968	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957471	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965392	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7974476	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974654	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7977365	0.83[AFR][1000 genomes]
rs9668610	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv826351	chr12:42584218-42676281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv826352	chr12:42593124-42675255	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10459290	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs10459290	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL
rs10459290	PPHLN1	cis	parietal	SCAN
rs10459290	GBA2	trans	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42550600-42615800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:42552400-42620000	Weak transcription	Fetal Brain Female	brain
3	chr12:42555000-42628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:42568400-42623400	Weak transcription	K562	blood
5	chr12:42568800-42630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:42569600-42630800	Weak transcription	Colonic Mucosa	Colon
7	chr12:42569800-42631000	Weak transcription	Gastric	stomach
8	chr12:42574800-42615600	Weak transcription	HUVEC	blood vessel
9	chr12:42575600-42628600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:42586800-42630000	Weak transcription	Fetal Kidney	kidney
11	chr12:42587200-42629600	Weak transcription	Lung	lung
12	chr12:42587400-42620000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:42587800-42619400	Weak transcription	Fetal Lung	lung
14	chr12:42587800-42623400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:42588400-42628600	Weak transcription	Thymus	Thymus
16	chr12:42591600-42628200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:42593200-42620000	Weak transcription	Dnd41	blood
18	chr12:42594000-42615400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:42594400-42615400	Weak transcription	Primary T cells from cord blood	blood
20	chr12:42602400-42628600	Weak transcription	Spleen	Spleen
21	chr12:42602400-42630800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:42602800-42628800	Weak transcription	HepG2	liver
23	chr12:42603000-42620200	Weak transcription	Primary B cells from cord blood	blood
24	chr12:42603600-42625800	Weak transcription	GM12878-XiMat	blood
25	chr12:42604400-42618800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:42604400-42619400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:42604400-42620000	Weak transcription	Liver	Liver
28	chr12:42604400-42623400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:42604400-42627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:42604400-42628000	Weak transcription	Placenta	Placenta
31	chr12:42604600-42615400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:42604600-42620000	Weak transcription	Brain Germinal Matrix	brain
33	chr12:42604600-42624400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:42604600-42626800	Weak transcription	Hela-S3	cervix
35	chr12:42604600-42628800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr12:42604600-42629000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:42605000-42615400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:42607200-42620000	Weak transcription	Fetal Thymus	thymus
39	chr12:42607800-42630600	Weak transcription	NHEK	skin
40	chr12:42608000-42614400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:42608000-42627400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:42608200-42614000	Weak transcription	Stomach Mucosa	stomach
43	chr12:42608200-42615600	Weak transcription	Fetal Intestine Large	intestine
44	chr12:42608200-42619400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:42608200-42620200	Weak transcription	Fetal Intestine Small	intestine
46	chr12:42608200-42624200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:42608200-42628600	Weak transcription	Brain Anterior Caudate	brain
48	chr12:42608200-42630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:42608400-42613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:42608400-42615200	Weak transcription	Small Intestine	intestine

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