Variant report

Variant	rs396360
Chromosome Location	chr6:13260453-13260454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13258722..13261158-chr6:13272393..13274593,2	K562	blood:
2	chr6:13259737..13263124-chr6:13265994..13271257,6	K562	blood:
3	chr6:13258559..13263124-chr6:13265994..13271116,8	K562	blood:
4	chr6:13260333..13262275-chr6:13263480..13265827,3	K562	blood:
5	chr6:13258722..13261158-chr6:13272026..13274593,3	K562	blood:

Variant related genes	Relation type
ENSG00000112137	Chromatin interaction
ENSG00000215022	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10948561	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12529141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665408	0.92[ASN][1000 genomes]
rs1569418	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16873893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1706941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736501	0.98[ASN][1000 genomes]
rs1736502	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs1937765	0.92[ASN][1000 genomes]
rs202024	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202026	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202055	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs202058	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs202059	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs202065	0.84[CHD][hapmap]
rs202067	0.87[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.92[EUR][1000 genomes]
rs34373947	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs393032	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]
rs413167	0.85[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs416852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426518	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs428975	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs429919	0.98[ASN][1000 genomes]
rs429935	0.98[ASN][1000 genomes]
rs430216	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs434703	0.98[ASN][1000 genomes]
rs436268	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs436490	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443150	0.98[ASN][1000 genomes]
rs4711945	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4711948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4711949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4711956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4715157	0.85[JPT][hapmap]
rs4715159	0.85[JPT][hapmap]
rs4715168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4715174	0.85[JPT][hapmap]
rs521960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs527857	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs533512	0.98[ASN][1000 genomes]
rs534266	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs534404	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534449	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs546673	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759256	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763251	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7765972	0.86[CHB][hapmap];1.00[CHD][hapmap];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
rs396360	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 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	chr6:13254200-13261200	Weak transcription	Lung	lung
9	chr6:13255800-13260800	Enhancers	Primary B cells from peripheral blood	blood
10	chr6:13256400-13266400	Weak transcription	Aorta	Aorta
11	chr6:13256600-13261200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:13256600-13266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:13256600-13267000	Weak transcription	Fetal Stomach	stomach
14	chr6:13256600-13268800	Weak transcription	Right Ventricle	heart
15	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
18	chr6:13256800-13262200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:13257000-13261800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:13257400-13263000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:13257600-13260600	Weak transcription	Adipose Nuclei	Adipose
22	chr6:13257600-13262200	Weak transcription	Liver	Liver
23	chr6:13258000-13263000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:13258600-13263400	Flanking Active TSS	GM12878-XiMat	blood
25	chr6:13258800-13272200	Weak transcription	Left Ventricle	heart
26	chr6:13259200-13261200	Weak transcription	Thymus	Thymus
27	chr6:13259400-13267400	Weak transcription	Fetal Heart	heart
28	chr6:13259600-13263400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:13259800-13260600	Enhancers	Brain Germinal Matrix	brain
30	chr6:13259800-13261000	Enhancers	Brain Substantia Nigra	brain
31	chr6:13259800-13261000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr6:13259800-13261800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:13259800-13262600	Enhancers	Primary T cells from cord blood	blood
34	chr6:13259800-13266800	Weak transcription	K562	blood
35	chr6:13260000-13261600	Enhancers	Brain Hippocampus Middle	brain
36	chr6:13260000-13262600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:13260200-13261000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:13260200-13261600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr6:13260200-13263600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:13260400-13260600	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:13260400-13261000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:13260400-13261200	Enhancers	Brain Anterior Caudate	brain
43	chr6:13260400-13261400	Enhancers	Brain Cingulate Gyrus	brain
44	chr6:13260400-13261600	Enhancers	Spleen	Spleen
45	chr6:13260400-13263600	Flanking Active TSS	Primary B cells from cord blood	blood

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