Variant report

Variant	rs9358858
Chromosome Location	chr6:25446308-25446309
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25445547..25447819-chr6:25452379..25454389,2	K562	blood:

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs72831267	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9348677	0.81[JPT][hapmap]
rs9358857	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366624	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9358858	GPX6	cis	cerebellum	SCAN
rs9358858	GMNN	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25411000-25451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:25416200-25447800	Weak transcription	Pancreas	Pancrea
3	chr6:25416600-25447800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:25418800-25462600	Weak transcription	Ovary	ovary
5	chr6:25432400-25447800	Weak transcription	Gastric	stomach
6	chr6:25433400-25472600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:25434200-25450200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:25435800-25447800	Weak transcription	Lung	lung
9	chr6:25436200-25481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:25438200-25472600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:25438400-25446400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:25440000-25447800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:25440600-25446800	Weak transcription	NHEK	skin
14	chr6:25442000-25455600	Weak transcription	Aorta	Aorta
15	chr6:25442200-25447200	Weak transcription	Stomach Mucosa	stomach
16	chr6:25442400-25449600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:25442600-25448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:25443200-25448200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:25443200-25472600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:25443600-25446800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:25444000-25446400	Weak transcription	Primary T cells from cord blood	blood
22	chr6:25444000-25447000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:25445000-25446600	Weak transcription	Left Ventricle	heart
24	chr6:25445200-25446800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr6:25445200-25447000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr6:25445200-25447600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:25445400-25446600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr6:25445400-25446600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr6:25445400-25446800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
30	chr6:25445800-25446600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
31	chr6:25445800-25446600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:25445800-25446600	ZNF genes & repeats	Fetal Thymus	thymus
33	chr6:25445800-25446800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:25445800-25446800	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr6:25445800-25447000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:25446000-25446600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:25446000-25446800	ZNF genes & repeats	Thymus	Thymus
38	chr6:25446000-25447000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:25446000-25447200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr6:25446000-25448000	Weak transcription	Right Atrium	heart
41	chr6:25446200-25446400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
42	chr6:25446200-25446400	ZNF genes & repeats	Fetal Brain Male	brain
43	chr6:25446200-25446600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
44	chr6:25446200-25446600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:25446200-25446600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
46	chr6:25446200-25446600	ZNF genes & repeats	Fetal Lung	lung
47	chr6:25446200-25446600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
48	chr6:25446200-25446800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:25446200-25446800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:25446200-25446800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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