Variant report

Variant	rs1059360
Chromosome Location	chr12:42554505-42554506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42548352..42550645-chr12:42552454..42554810,2	MCF-7	breast:
2	chr12:42552974..42555837-chr12:42630405..42632767,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10459290	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]
rs10492388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880256	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880258	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880259	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880260	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880261	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880264	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880269	0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880272	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880273	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181328	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs11181364	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181378	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11181380	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181398	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181399	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11181422	0.83[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12049942	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12308219	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12366848	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12370778	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12371615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12371762	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178753	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs2406567	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406568	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406674	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[TSI][hapmap]
rs3229	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap]
rs3747557	0.81[CHB][hapmap]
rs3747560	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs3810793	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[TSI][hapmap]
rs4768399	0.84[CEU][hapmap]
rs6582390	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582391	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582395	0.84[CEU][hapmap]
rs7138877	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312933	0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap]
rs7315968	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957471	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965392	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7974476	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7974654	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9668610	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1059360	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL
rs1059360	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs1059360	PPHLN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
4	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:42539600-42555800	Weak transcription	Brain Substantia Nigra	brain
6	chr12:42539600-42556200	Weak transcription	HSMMtube	muscle
7	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
9	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:42539800-42568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:42539800-42569000	Weak transcription	Fetal Kidney	kidney
12	chr12:42539800-42582800	Weak transcription	Spleen	Spleen
13	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
14	chr12:42540000-42556000	Weak transcription	Fetal Intestine Small	intestine
15	chr12:42540000-42574800	Weak transcription	Brain Anterior Caudate	brain
16	chr12:42546000-42564400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:42547200-42563800	Weak transcription	Fetal Stomach	stomach
18	chr12:42547800-42610400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:42549400-42575000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:42550200-42555400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:42550400-42556200	Weak transcription	Fetal Heart	heart
22	chr12:42550600-42555200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:42550600-42557400	Weak transcription	Colonic Mucosa	Colon
24	chr12:42550600-42615800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:42550800-42555600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:42550800-42568400	Weak transcription	Right Ventricle	heart
27	chr12:42551400-42554800	Strong transcription	Primary B cells from cord blood	blood
28	chr12:42551400-42557800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:42551600-42555200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:42551800-42555200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:42551800-42555400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:42551800-42555400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:42551800-42555400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:42551800-42555600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:42552000-42556000	Weak transcription	HMEC	breast
36	chr12:42552000-42604000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:42552200-42554800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:42552200-42555000	Strong transcription	HSMM	muscle
39	chr12:42552200-42555400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:42552200-42555800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:42552200-42557400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:42552200-42574800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:42552200-42591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:42552200-42613000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:42552400-42555600	Strong transcription	Dnd41	blood
46	chr12:42552400-42620000	Weak transcription	Fetal Brain Female	brain
47	chr12:42552600-42578800	Weak transcription	Lung	lung
48	chr12:42552800-42556000	Weak transcription	NHLF	lung
49	chr12:42552800-42564400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:42553000-42555000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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