Variant report

Variant	rs428975
Chromosome Location	chr6:13256375-13256376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10948561	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12525892	0.98[ASN][1000 genomes]
rs12525906	0.98[ASN][1000 genomes]
rs12527600	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12529141	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665408	0.92[ASN][1000 genomes]
rs1569418	0.88[ASN][1000 genomes]
rs16873893	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1706941	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736501	0.98[ASN][1000 genomes]
rs1736502	0.96[ASN][1000 genomes]
rs1937765	0.92[ASN][1000 genomes]
rs202024	0.98[ASN][1000 genomes]
rs202026	0.98[ASN][1000 genomes]
rs202055	0.94[ASN][1000 genomes]
rs202058	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs202059	0.92[ASN][1000 genomes]
rs202067	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34373947	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs393032	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs396360	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs413167	0.98[ASN][1000 genomes]
rs416852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426518	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs429919	0.98[ASN][1000 genomes]
rs429935	0.98[ASN][1000 genomes]
rs430216	0.98[ASN][1000 genomes]
rs434703	0.98[ASN][1000 genomes]
rs436268	0.98[ASN][1000 genomes]
rs436490	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443150	0.98[ASN][1000 genomes]
rs4711945	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4711948	0.98[ASN][1000 genomes]
rs4711949	0.98[ASN][1000 genomes]
rs4711956	0.98[ASN][1000 genomes]
rs4715168	0.92[ASN][1000 genomes]
rs527857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs533512	0.98[ASN][1000 genomes]
rs534266	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs534404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534449	0.96[ASN][1000 genomes]
rs546673	0.92[AFR][1000 genomes];0.99[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	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759256	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763251	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7765972	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
rs428975	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 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	chr6:13248600-13256600	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:13248600-13260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:13248800-13266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:13249000-13257800	Weak transcription	Brain Anterior Caudate	brain
6	chr6:13249000-13266000	Weak transcription	Fetal Brain Female	brain
7	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:13249600-13256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
10	chr6:13251000-13259000	Weak transcription	Fetal Heart	heart
11	chr6:13251400-13256400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:13252800-13257600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr6:13253000-13264200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:13254000-13256400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:13254000-13260200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:13254000-13265400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:13254200-13256600	Weak transcription	HepG2	liver
18	chr6:13254200-13261200	Weak transcription	Lung	lung
19	chr6:13254600-13256600	ZNF genes & repeats	Liver	Liver
20	chr6:13254800-13256400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:13254800-13256600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:13255400-13256400	Strong transcription	Aorta	Aorta
23	chr6:13255600-13256600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr6:13255800-13256600	Enhancers	Left Ventricle	heart
25	chr6:13255800-13260800	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:13256000-13256400	Enhancers	Spleen	Spleen
27	chr6:13256000-13256600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:13256000-13256600	Enhancers	Pancreas	Pancrea
29	chr6:13256000-13256600	Enhancers	Right Ventricle	heart
30	chr6:13256000-13256600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr6:13256000-13256800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:13256000-13257600	ZNF genes & repeats	GM12878-XiMat	blood
33	chr6:13256000-13258000	Strong transcription	Primary hematopoietic stem cells	blood
34	chr6:13256000-13260400	Enhancers	Primary B cells from cord blood	blood
35	chr6:13256200-13256600	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr6:13256200-13256600	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:13256200-13256600	Enhancers	Fetal Muscle Trunk	muscle
38	chr6:13256200-13256600	ZNF genes & repeats	Fetal Stomach	stomach
39	chr6:13256200-13257600	ZNF genes & repeats	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links