Variant report

Variant	rs4711949
Chromosome Location	chr6:13254098-13254099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13253939..13256306-chr6:13258215..13259819,2	K562	blood:
2	chr6:13252536..13255335-chr6:13260574..13262667,2	K562	blood:
3	chr6:13253507..13255160-chr6:13298362..13301055,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1014820	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10948550	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948561	1.00[ASN][1000 genomes]
rs11751747	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11755185	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11963839	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11966270	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11967582	0.90[EUR][1000 genomes]
rs11968818	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11969387	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525681	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12525892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527422	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12527600	1.00[ASN][1000 genomes]
rs12527775	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12528951	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12528966	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12529141	1.00[ASN][1000 genomes]
rs12660341	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12660392	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12660606	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12661071	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12665408	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12665414	0.90[EUR][1000 genomes]
rs12665416	0.90[EUR][1000 genomes]
rs1569418	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16873893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1706941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175729	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17667989	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs1937765	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202026	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202031	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs202033	0.89[AMR][1000 genomes]
rs202037	0.89[AMR][1000 genomes]
rs202043	0.92[AMR][1000 genomes]
rs202049	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs202052	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202055	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202056	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs202057	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs202059	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202061	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202062	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs202063	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs202065	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202067	0.82[JPT][hapmap]
rs202075	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202076	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs202078	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2142568	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34275015	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs364419	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs369946	0.89[AMR][1000 genomes]
rs377019	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs393032	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs396360	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs413167	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416852	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs417024	0.89[AMR][1000 genomes]
rs428975	0.98[ASN][1000 genomes]
rs429919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434923	0.89[AMR][1000 genomes]
rs436268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436490	1.00[ASN][1000 genomes]
rs443150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711946	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4711948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715154	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715155	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4715157	0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs4715158	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4715159	0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs4715168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715174	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715183	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715184	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs521960	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs527857	1.00[ASN][1000 genomes]
rs533512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534404	1.00[ASN][1000 genomes]
rs534449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs546673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs555496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58474010	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59566077	0.90[EUR][1000 genomes]
rs595864	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs602976	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs603394	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs644309	0.89[AMR][1000 genomes]
rs73355358	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73355362	0.95[EUR][1000 genomes]
rs73355368	0.95[EUR][1000 genomes]
rs7759256	0.85[JPT][hapmap]
rs7765972	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4711949	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13233200-13256000	Weak transcription	Right Ventricle	heart
2	chr6:13234600-13267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:13242800-13256000	Weak transcription	Pancreas	Pancrea
4	chr6:13248600-13256600	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:13248600-13260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:13248800-13256200	Weak transcription	Brain Germinal Matrix	brain
7	chr6:13248800-13266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:13249000-13257800	Weak transcription	Brain Anterior Caudate	brain
9	chr6:13249000-13266000	Weak transcription	Fetal Brain Female	brain
10	chr6:13249200-13254400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:13249600-13256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
14	chr6:13251000-13259000	Weak transcription	Fetal Heart	heart
15	chr6:13251400-13256400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:13251800-13255800	Weak transcription	Left Ventricle	heart
17	chr6:13252800-13257600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:13253000-13254200	Enhancers	Primary B cells from cord blood	blood
19	chr6:13253000-13254200	Enhancers	Primary B cells from peripheral blood	blood
20	chr6:13253000-13254200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr6:13253000-13264200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:13253200-13254200	Strong transcription	Aorta	Aorta
23	chr6:13253200-13254600	Enhancers	Primary hematopoietic stem cells	blood
24	chr6:13253200-13254800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:13253200-13256000	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr6:13253400-13254200	Enhancers	Lung	lung
27	chr6:13253600-13254200	Enhancers	HepG2	liver
28	chr6:13253800-13256000	Weak transcription	Spleen	Spleen
29	chr6:13254000-13254800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:13254000-13256400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:13254000-13260200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:13254000-13265400	Weak transcription	Stomach Smooth Muscle	stomach

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