Variant report

Variant	rs1937765
Chromosome Location	chr6:13234508-13234509
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	chr6:13232923..13234560-chr6:13313162..13315905,2	K562	blood:
2	chr6:13233464..13235028-chr6:13327607..13330085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1014820	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948550	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948561	0.94[ASN][1000 genomes]
rs11751747	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11755185	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11963839	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11966270	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11967582	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11968818	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11969387	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525681	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525892	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12525906	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12527422	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12527600	0.94[ASN][1000 genomes]
rs12527775	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12528951	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12528966	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12529141	0.94[ASN][1000 genomes]
rs12660341	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12660392	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12660606	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12661071	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12665408	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665414	0.90[EUR][1000 genomes]
rs12665416	0.90[EUR][1000 genomes]
rs1569418	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16873893	0.90[ASN][1000 genomes]
rs1706941	0.94[ASN][1000 genomes]
rs1736501	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1736502	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs175729	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17667989	0.84[AMR][1000 genomes]
rs202024	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202026	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202031	0.84[AMR][1000 genomes]
rs202033	0.84[AMR][1000 genomes]
rs202037	0.84[AMR][1000 genomes]
rs202043	0.87[AMR][1000 genomes]
rs202049	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs202052	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202055	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202056	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs202057	0.85[EUR][1000 genomes]
rs202059	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202061	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202062	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202063	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202065	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202075	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202076	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs202078	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2142568	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34275015	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs364419	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs369946	0.84[AMR][1000 genomes]
rs377019	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs393032	0.92[ASN][1000 genomes]
rs396360	0.92[ASN][1000 genomes]
rs413167	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs416852	0.94[ASN][1000 genomes]
rs417024	0.84[AMR][1000 genomes]
rs428975	0.92[ASN][1000 genomes]
rs429919	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429935	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs430216	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434703	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434923	0.84[AMR][1000 genomes]
rs436268	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs436490	0.94[ASN][1000 genomes]
rs443150	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711946	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711948	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711949	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711956	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715154	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715155	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715157	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715158	0.90[EUR][1000 genomes]
rs4715159	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715168	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715174	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715183	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715184	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs527857	0.94[ASN][1000 genomes]
rs533512	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs534404	0.94[ASN][1000 genomes]
rs534449	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs546673	0.92[ASN][1000 genomes]
rs555496	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58474010	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59566077	0.90[EUR][1000 genomes]
rs595864	0.94[ASN][1000 genomes]
rs602976	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs603394	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs644309	0.84[AMR][1000 genomes]
rs73355358	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73355362	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73355368	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7765972	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432849	chr6:13225077-13253733	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1937765	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13208200-13239800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:13217800-13242400	Weak transcription	Pancreas	Pancrea
3	chr6:13218200-13235000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:13218400-13241000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:13227800-13235600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:13227800-13238600	Strong transcription	Stomach Smooth Muscle	stomach
7	chr6:13227800-13240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:13228000-13236000	Weak transcription	Fetal Brain Male	brain
10	chr6:13228400-13237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:13229200-13240000	Weak transcription	Fetal Lung	lung
12	chr6:13229400-13248200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:13230000-13236000	Strong transcription	Brain Anterior Caudate	brain
14	chr6:13230000-13239800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:13230200-13235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:13230200-13242400	Weak transcription	Fetal Intestine Small	intestine
17	chr6:13230600-13253400	Weak transcription	Spleen	Spleen
18	chr6:13230800-13248000	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:13231200-13248200	Weak transcription	Fetal Stomach	stomach
20	chr6:13232200-13235600	Strong transcription	Lung	lung
21	chr6:13232800-13239800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:13232800-13240000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:13232800-13240200	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:13232800-13243800	Weak transcription	Fetal Brain Female	brain
25	chr6:13233200-13234600	Enhancers	Placenta	Placenta
26	chr6:13233200-13236200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:13233200-13239800	Weak transcription	Brain Angular Gyrus	brain
28	chr6:13233200-13256000	Weak transcription	Right Ventricle	heart
29	chr6:13233400-13236000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:13233600-13236600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:13234000-13234600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:13234000-13234600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:13234000-13234800	Genic enhancers	Fetal Heart	heart
34	chr6:13234000-13234800	Enhancers	GM12878-XiMat	blood
35	chr6:13234000-13235200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:13234000-13235200	Enhancers	HSMMtube	muscle
37	chr6:13234000-13236000	Strong transcription	Brain Germinal Matrix	brain
38	chr6:13234000-13236200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:13234200-13234600	Enhancers	Aorta	Aorta
40	chr6:13234200-13234800	Enhancers	HMEC	breast
41	chr6:13234200-13235200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:13234200-13235400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:13234200-13235600	Enhancers	Liver	Liver
44	chr6:13234200-13235600	Enhancers	NHDF-Ad	bronchial
45	chr6:13234400-13234800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:13234400-13236200	Weak transcription	Left Ventricle	heart

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