Variant report

Variant	rs12049942
Chromosome Location	chr12:42587052-42587053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42586906..42588789-chr12:42631235..42632945,2	MCF-7	breast:
2	chr12:42586733..42589721-chr12:42593735..42596907,3	MCF-7	breast:
3	chr12:42584441..42587115-chr12:42588647..42591511,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10459290	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10492388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1059360	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785334	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880256	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880258	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880260	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880269	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880272	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880273	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181380	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181398	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181399	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12308219	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12366848	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12370778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12371615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371762	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2406567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406568	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582390	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6582391	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315968	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957471	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7965392	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7974476	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974654	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9668610	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[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	nsv437751	chr12:42586641-42599122	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12049942	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL
rs12049942	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
2	chr12:42547800-42610400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:42550600-42615800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:42552000-42604000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:42552200-42591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:42552200-42613000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:42552400-42620000	Weak transcription	Fetal Brain Female	brain
8	chr12:42553600-42590000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:42554000-42607600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:42554600-42592200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:42555000-42628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:42555200-42590000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:42555400-42598000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:42556800-42613200	Weak transcription	HMEC	breast
15	chr12:42557000-42604000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:42557200-42606800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:42558000-42602400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:42563200-42608000	Weak transcription	Small Intestine	intestine
19	chr12:42565400-42587400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:42566000-42588600	Weak transcription	Placenta	Placenta
21	chr12:42568400-42623400	Weak transcription	K562	blood
22	chr12:42568600-42607800	Weak transcription	Right Ventricle	heart
23	chr12:42568800-42630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:42569600-42630800	Weak transcription	Colonic Mucosa	Colon
25	chr12:42569800-42631000	Weak transcription	Gastric	stomach
26	chr12:42570800-42589400	Weak transcription	HSMMtube	muscle
27	chr12:42571400-42591200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:42571400-42597600	Weak transcription	Esophagus	oesophagus
29	chr12:42571600-42602400	Weak transcription	HepG2	liver
30	chr12:42573000-42589400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:42573400-42587200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:42574800-42615600	Weak transcription	HUVEC	blood vessel
33	chr12:42575400-42591000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:42575600-42590000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:42575600-42607800	Weak transcription	Brain Angular Gyrus	brain
36	chr12:42575600-42628600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:42575800-42607800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:42575800-42607800	Weak transcription	Brain Substantia Nigra	brain
39	chr12:42576000-42591800	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:42576200-42592400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:42576600-42607800	Weak transcription	Brain Anterior Caudate	brain
42	chr12:42578000-42606400	Weak transcription	Fetal Heart	heart
43	chr12:42578400-42591000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:42578800-42603600	Weak transcription	Brain Germinal Matrix	brain
45	chr12:42579000-42589600	Weak transcription	Left Ventricle	heart
46	chr12:42579000-42590600	Weak transcription	Psoas Muscle	Psoas
47	chr12:42579200-42590600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:42579200-42606800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:42579400-42588200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:42579400-42588800	Weak transcription	Fetal Thymus	thymus

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