Variant report

Variant	rs534266
Chromosome Location	chr6:13256700-13256701
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1014820	0.81[ASN][1000 genomes]
rs10948550	0.86[ASN][1000 genomes]
rs10948561	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11751747	0.86[ASN][1000 genomes]
rs11755185	0.86[ASN][1000 genomes]
rs11963839	0.80[ASN][1000 genomes]
rs11966270	0.86[ASN][1000 genomes]
rs11968818	0.80[ASN][1000 genomes]
rs11969387	0.86[ASN][1000 genomes]
rs12525681	0.86[ASN][1000 genomes]
rs12527422	0.86[ASN][1000 genomes]
rs12527600	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12527775	0.86[ASN][1000 genomes]
rs12528951	0.86[ASN][1000 genomes]
rs12528966	0.86[ASN][1000 genomes]
rs12529141	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12660341	0.86[ASN][1000 genomes]
rs12660392	0.86[ASN][1000 genomes]
rs12660606	0.86[ASN][1000 genomes]
rs12661071	0.84[ASN][1000 genomes]
rs16873855	0.86[ASN][1000 genomes]
rs16873893	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1706941	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs175729	0.86[ASN][1000 genomes]
rs202057	0.81[ASN][1000 genomes]
rs202058	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs202061	0.86[ASN][1000 genomes]
rs202062	0.84[ASN][1000 genomes]
rs202063	0.86[ASN][1000 genomes]
rs202067	0.91[EUR][1000 genomes]
rs2142568	0.80[ASN][1000 genomes]
rs34275015	0.86[ASN][1000 genomes]
rs34373947	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs364419	0.84[ASN][1000 genomes]
rs366332	0.80[EUR][1000 genomes]
rs368590	0.80[EUR][1000 genomes]
rs377019	0.86[ASN][1000 genomes]
rs393032	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs396360	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs408284	0.80[EUR][1000 genomes]
rs416831	0.80[EUR][1000 genomes]
rs416852	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs426518	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs428975	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs436490	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs449321	0.80[EUR][1000 genomes]
rs450025	0.80[EUR][1000 genomes]
rs452021	0.80[EUR][1000 genomes]
rs45450	0.80[EUR][1000 genomes]
rs4711945	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711946	0.86[ASN][1000 genomes]
rs4715174	0.80[ASN][1000 genomes]
rs4715183	0.86[ASN][1000 genomes]
rs4715184	0.86[ASN][1000 genomes]
rs527857	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs534404	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs546017	0.80[EUR][1000 genomes]
rs546673	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs595864	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs602976	0.86[ASN][1000 genomes]
rs603394	0.86[ASN][1000 genomes]
rs73355358	0.86[ASN][1000 genomes]
rs73355362	0.84[ASN][1000 genomes]
rs73355368	0.86[ASN][1000 genomes]
rs7759256	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7763251	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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
rs534266	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13234600-13267200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:13248600-13260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:13248800-13266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13249000-13257800	Weak transcription	Brain Anterior Caudate	brain
5	chr6:13249000-13266000	Weak transcription	Fetal Brain Female	brain
6	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
8	chr6:13251000-13259000	Weak transcription	Fetal Heart	heart
9	chr6:13252800-13257600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr6:13253000-13264200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:13254000-13260200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:13254000-13265400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:13254200-13261200	Weak transcription	Lung	lung
14	chr6:13255800-13260800	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:13256000-13256800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:13256000-13257600	ZNF genes & repeats	GM12878-XiMat	blood
17	chr6:13256000-13258000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr6:13256000-13260400	Enhancers	Primary B cells from cord blood	blood
19	chr6:13256200-13257600	ZNF genes & repeats	Adipose Nuclei	Adipose
20	chr6:13256400-13256800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:13256400-13257000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:13256400-13257000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:13256400-13257400	Enhancers	K562	blood
24	chr6:13256400-13266400	Weak transcription	Aorta	Aorta
25	chr6:13256600-13256800	Flanking Active TSS	Liver	Liver
26	chr6:13256600-13257000	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr6:13256600-13257200	Enhancers	HepG2	liver
28	chr6:13256600-13257400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:13256600-13257400	Enhancers	Brain Hippocampus Middle	brain
30	chr6:13256600-13258000	Weak transcription	Left Ventricle	heart
31	chr6:13256600-13259800	Weak transcription	Brain Germinal Matrix	brain
32	chr6:13256600-13260000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:13256600-13260400	Weak transcription	Spleen	Spleen
34	chr6:13256600-13261200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:13256600-13266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:13256600-13267000	Weak transcription	Fetal Stomach	stomach
37	chr6:13256600-13268800	Weak transcription	Right Ventricle	heart
38	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea

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