Variant report

Variant	rs393032
Chromosome Location	chr6:13261256-13261257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13252536..13255335-chr6:13260574..13262667,2	K562	blood:
2	chr6:13260473..13261996-chr6:13328125..13330336,2	K562	blood:
3	chr6:13259737..13263124-chr6:13265994..13271257,6	K562	blood:
4	chr6:13258559..13263124-chr6:13265994..13271116,8	K562	blood:
5	chr6:13260333..13262275-chr6:13263480..13265827,3	K562	blood:

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10948561	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11968818	0.85[JPT][hapmap]
rs12525892	0.98[ASN][1000 genomes]
rs12525906	0.98[ASN][1000 genomes]
rs12527600	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12529141	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665408	0.92[ASN][1000 genomes]
rs1569418	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16873893	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1706941	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736501	0.98[ASN][1000 genomes]
rs1736502	0.85[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs1937765	0.92[ASN][1000 genomes]
rs202024	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202026	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202055	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs202058	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs202059	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs202067	0.85[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34373947	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs366332	0.87[CEU][hapmap]
rs396360	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408284	0.86[CEU][hapmap]
rs413167	1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs416852	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426518	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs428975	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs429919	0.98[ASN][1000 genomes]
rs429935	0.98[ASN][1000 genomes]
rs430216	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs434703	0.98[ASN][1000 genomes]
rs435466	0.85[CEU][hapmap]
rs436268	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs436490	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443150	0.98[ASN][1000 genomes]
rs449321	0.85[CEU][hapmap]
rs45450	0.85[CEU][hapmap]
rs4711945	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711948	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4711949	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4711956	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4715157	0.85[JPT][hapmap]
rs4715159	0.85[JPT][hapmap]
rs4715168	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4715174	0.85[JPT][hapmap]
rs521960	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs527857	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs533512	0.98[ASN][1000 genomes]
rs534266	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs534404	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534449	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs546673	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555496	0.90[ASN][1000 genomes]
rs58474010	0.88[ASN][1000 genomes]
rs595864	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759256	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7763251	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7765972	1.00[JPT][hapmap];0.92[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
rs393032	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:50 , 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	chr6:13248800-13266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:13249000-13266000	Weak transcription	Fetal Brain Female	brain
4	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
6	chr6:13253000-13264200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:13254000-13265400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:13256400-13266400	Weak transcription	Aorta	Aorta
9	chr6:13256600-13266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:13256600-13267000	Weak transcription	Fetal Stomach	stomach
11	chr6:13256600-13268800	Weak transcription	Right Ventricle	heart
12	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
15	chr6:13256800-13262200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:13257000-13261800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:13257400-13263000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:13257600-13262200	Weak transcription	Liver	Liver
19	chr6:13258000-13263000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:13258600-13263400	Flanking Active TSS	GM12878-XiMat	blood
21	chr6:13258800-13272200	Weak transcription	Left Ventricle	heart
22	chr6:13259400-13267400	Weak transcription	Fetal Heart	heart
23	chr6:13259600-13263400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:13259800-13261800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:13259800-13262600	Enhancers	Primary T cells from cord blood	blood
26	chr6:13259800-13266800	Weak transcription	K562	blood
27	chr6:13260000-13261600	Enhancers	Brain Hippocampus Middle	brain
28	chr6:13260000-13262600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:13260200-13261600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:13260200-13263600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:13260400-13261400	Enhancers	Brain Cingulate Gyrus	brain
32	chr6:13260400-13261600	Enhancers	Spleen	Spleen
33	chr6:13260400-13263600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr6:13260600-13266600	Weak transcription	Brain Germinal Matrix	brain
35	chr6:13260800-13262600	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr6:13261000-13263000	Weak transcription	Brain Substantia Nigra	brain
37	chr6:13261000-13263200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr6:13261000-13263400	Enhancers	Primary hematopoietic stem cells	blood
39	chr6:13261000-13265800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:13261000-13266600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:13261000-13268800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:13261200-13261400	Enhancers	Adipose Nuclei	Adipose
43	chr6:13261200-13261400	Enhancers	Brain Angular Gyrus	brain
44	chr6:13261200-13261400	Enhancers	Duodenum Mucosa	Duodenum
45	chr6:13261200-13261400	ZNF genes & repeats	Lung	lung
46	chr6:13261200-13262000	Enhancers	Right Atrium	heart
47	chr6:13261200-13262200	Enhancers	Thymus	Thymus
48	chr6:13261200-13262400	Weak transcription	Brain Anterior Caudate	brain
49	chr6:13261200-13262600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:13261200-13263000	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links