Variant report

Variant	rs11969387
Chromosome Location	chr6:13233169-13233170
allele	A/C
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:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1014820	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963839	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11966270	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967582	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11968818	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12525681	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525892	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525906	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12527422	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528966	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665408	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12665414	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665416	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1569418	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16873855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1736501	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1736502	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs175729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17667989	0.82[CEU][hapmap]
rs1937765	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202024	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202026	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202031	0.82[CEU][hapmap]
rs202055	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202056	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202057	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs202059	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202065	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs202075	0.88[EUR][1000 genomes]
rs202076	0.86[EUR][1000 genomes]
rs202078	0.82[EUR][1000 genomes]
rs2142568	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34275015	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34373947	1.00[ASN][1000 genomes]
rs364419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377019	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413167	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs426518	0.90[JPT][hapmap]
rs429919	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs429935	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs430216	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs434703	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs436268	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs443150	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4711946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711948	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711949	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711956	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715154	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715157	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715158	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715159	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715168	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715174	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4715183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533512	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs534266	0.86[ASN][1000 genomes]
rs534449	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs555496	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58474010	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59566077	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs602976	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73355358	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73355362	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73355368	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759256	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs7763251	0.89[ASN][1000 genomes]
rs7765972	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][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
rs11969387	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 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	chr6:13218600-13234400	Weak transcription	HSMM	muscle
6	chr6:13227800-13233200	Strong transcription	Left Ventricle	heart
7	chr6:13227800-13235600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:13227800-13238600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr6:13227800-13240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:13227800-13244000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:13228000-13236000	Weak transcription	Fetal Brain Male	brain
12	chr6:13228400-13237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:13229200-13240000	Weak transcription	Fetal Lung	lung
14	chr6:13229400-13248200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:13229600-13233200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:13229600-13233200	Strong transcription	Aorta	Aorta
17	chr6:13230000-13233200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:13230000-13233200	Strong transcription	Brain Angular Gyrus	brain
19	chr6:13230000-13233400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:13230000-13236000	Strong transcription	Brain Anterior Caudate	brain
21	chr6:13230000-13239800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:13230200-13234200	Weak transcription	Liver	Liver
23	chr6:13230200-13235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:13230200-13242400	Weak transcription	Fetal Intestine Small	intestine
25	chr6:13230600-13233200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:13230600-13234200	Weak transcription	NHDF-Ad	bronchial
27	chr6:13230600-13253400	Weak transcription	Spleen	Spleen
28	chr6:13230800-13248000	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:13231000-13234000	Weak transcription	HSMMtube	muscle
30	chr6:13231200-13248200	Weak transcription	Fetal Stomach	stomach
31	chr6:13231800-13233600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr6:13232000-13233400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:13232200-13235600	Strong transcription	Lung	lung
34	chr6:13232400-13233200	Strong transcription	Right Ventricle	heart
35	chr6:13232400-13234000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:13232600-13234000	Weak transcription	GM12878-XiMat	blood
37	chr6:13232800-13234000	Weak transcription	Brain Germinal Matrix	brain
38	chr6:13232800-13239800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:13232800-13240000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:13232800-13240200	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:13232800-13243800	Weak transcription	Fetal Brain Female	brain
42	chr6:13233000-13234000	Weak transcription	Fetal Heart	heart

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