Variant report

Variant	rs4711945
Chromosome Location	chr6:13235072-13235073
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13234560..13237159-chr6:13237392..13240503,3	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1014820	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10948550	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10948561	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11751747	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11755185	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11963839	0.88[ASN][1000 genomes]
rs11966270	1.00[ASN][1000 genomes]
rs11967582	0.82[ASN][1000 genomes]
rs11968818	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs11969387	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12525681	1.00[ASN][1000 genomes]
rs12527422	1.00[ASN][1000 genomes]
rs12527600	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12527775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12528951	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12528966	1.00[ASN][1000 genomes]
rs12529141	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12660341	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12660392	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12660606	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12661071	0.98[ASN][1000 genomes]
rs12665414	0.90[ASN][1000 genomes]
rs12665416	0.90[ASN][1000 genomes]
rs16873855	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16873893	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1706941	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs175729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs202058	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs202061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs202062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202063	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs202065	0.90[JPT][hapmap]
rs202067	0.86[EUR][1000 genomes]
rs2142568	0.88[ASN][1000 genomes]
rs34275015	1.00[ASN][1000 genomes]
rs34373947	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs377019	1.00[ASN][1000 genomes]
rs393032	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs396360	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs416852	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426518	0.90[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs428975	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs436490	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4711946	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4715154	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4715155	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4715157	0.82[ASN][1000 genomes]
rs4715158	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4715159	0.82[ASN][1000 genomes]
rs4715174	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs4715183	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4715184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs527857	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs534266	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs534404	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs546673	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59566077	0.91[ASN][1000 genomes]
rs595864	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs602976	1.00[ASN][1000 genomes]
rs603394	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73355358	1.00[ASN][1000 genomes]
rs73355362	0.98[ASN][1000 genomes]
rs73355368	1.00[ASN][1000 genomes]
rs7759256	0.92[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7763251	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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
rs4711945	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 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	chr6:13218400-13241000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:13227800-13235600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:13227800-13238600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr6:13227800-13240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:13228000-13236000	Weak transcription	Fetal Brain Male	brain
9	chr6:13228400-13237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:13229200-13240000	Weak transcription	Fetal Lung	lung
11	chr6:13229400-13248200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:13230000-13236000	Strong transcription	Brain Anterior Caudate	brain
13	chr6:13230000-13239800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:13230200-13242400	Weak transcription	Fetal Intestine Small	intestine
15	chr6:13230600-13253400	Weak transcription	Spleen	Spleen
16	chr6:13230800-13248000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:13231200-13248200	Weak transcription	Fetal Stomach	stomach
18	chr6:13232200-13235600	Strong transcription	Lung	lung
19	chr6:13232800-13239800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:13232800-13240000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:13232800-13240200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:13232800-13243800	Weak transcription	Fetal Brain Female	brain
23	chr6:13233200-13236200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:13233200-13239800	Weak transcription	Brain Angular Gyrus	brain
25	chr6:13233200-13256000	Weak transcription	Right Ventricle	heart
26	chr6:13233400-13236000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:13233600-13236600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:13234000-13235200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:13234000-13235200	Enhancers	HSMMtube	muscle
30	chr6:13234000-13236000	Strong transcription	Brain Germinal Matrix	brain
31	chr6:13234000-13236200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:13234200-13235200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:13234200-13235400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:13234200-13235600	Enhancers	Liver	Liver
35	chr6:13234200-13235600	Enhancers	NHDF-Ad	bronchial
36	chr6:13234400-13236200	Weak transcription	Left Ventricle	heart
37	chr6:13234600-13238800	Weak transcription	Aorta	Aorta
38	chr6:13234600-13239800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:13234600-13267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:13234800-13236600	Weak transcription	Fetal Heart	heart

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