Variant report

Variant	rs11966270
Chromosome Location	chr6:13239101-13239102
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13238401..13240269-chr6:13241272..13242998,2	K562	blood:
2	chr6:13224141..13226448-chr6:13237492..13239981,3	K562	blood:
3	chr6:13234560..13237159-chr6:13237392..13240503,3	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1014820	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948550	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751747	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755185	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963839	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11967582	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11968818	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11969387	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525681	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525892	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12525906	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12527422	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527775	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528951	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528966	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660341	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660392	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660606	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661071	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665408	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12665414	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665416	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1569418	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16873855	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1736501	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1736502	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs175729	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937765	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202024	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202026	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202052	0.81[EUR][1000 genomes]
rs202055	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202056	0.97[EUR][1000 genomes]
rs202057	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs202059	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202061	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202062	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202063	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202065	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs202075	0.90[EUR][1000 genomes]
rs202076	0.88[EUR][1000 genomes]
rs202078	0.84[EUR][1000 genomes]
rs2142568	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34275015	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34373947	1.00[ASN][1000 genomes]
rs364419	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377019	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413167	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs429919	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs429935	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs430216	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs434703	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs436268	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs443150	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4711945	1.00[ASN][1000 genomes]
rs4711946	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711948	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4711949	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4711956	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715154	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715155	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715157	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715158	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715159	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715168	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715174	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4715183	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715184	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533512	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs534266	0.86[ASN][1000 genomes]
rs534449	0.97[EUR][1000 genomes]
rs555496	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58474010	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59566077	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs602976	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603394	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73355358	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73355362	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73355368	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759256	0.88[ASN][1000 genomes]
rs7763251	0.89[ASN][1000 genomes]
rs7765972	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	esv1815942	chr6:13235495-13250588	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1817130	chr6:13235495-13250588	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1830412	chr6:13235495-13250588	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1832850	chr6:13235495-13250588	Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1846185	chr6:13235495-13250588	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1848354	chr6:13235495-13250588	Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
10	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11966270	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 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	chr6:13227800-13240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:13229200-13240000	Weak transcription	Fetal Lung	lung
7	chr6:13229400-13248200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:13230000-13239800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:13230200-13242400	Weak transcription	Fetal Intestine Small	intestine
10	chr6:13230600-13253400	Weak transcription	Spleen	Spleen
11	chr6:13230800-13248000	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:13231200-13248200	Weak transcription	Fetal Stomach	stomach
13	chr6:13232800-13239800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:13232800-13240000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:13232800-13240200	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:13232800-13243800	Weak transcription	Fetal Brain Female	brain
17	chr6:13233200-13239800	Weak transcription	Brain Angular Gyrus	brain
18	chr6:13233200-13256000	Weak transcription	Right Ventricle	heart
19	chr6:13234600-13239800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:13234600-13267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:13235200-13239800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:13235200-13248200	Weak transcription	HSMMtube	muscle
23	chr6:13235600-13240000	Weak transcription	Lung	lung
24	chr6:13236000-13248000	Weak transcription	Brain Germinal Matrix	brain
25	chr6:13236200-13239400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:13236800-13239200	Weak transcription	Left Ventricle	heart
27	chr6:13237000-13243800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:13237400-13239600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:13237600-13252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:13238000-13239200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:13238200-13240000	Enhancers	Fetal Heart	heart
32	chr6:13238600-13239600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:13238800-13239600	Weak transcription	Brain Anterior Caudate	brain
34	chr6:13239000-13240200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:13239000-13241600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:13239000-13253200	Weak transcription	Aorta	Aorta

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