Variant report

Variant	rs12342465
Chromosome Location	chr9:108212096-108212097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108207991..108210582-chr9:108211502..108213695,2	K562	blood:

Variant related genes	Relation type
ENSG00000106701	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10991660	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10991682	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13362922	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1808155	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2149592	0.83[AFR][1000 genomes]
rs2149593	0.86[AFR][1000 genomes]
rs7033452	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7034699	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7034702	0.86[AFR][1000 genomes]
rs7867012	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7870485	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7872832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9969773	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108209800-108212200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:108209800-108212400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:108209800-108212800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:108210000-108212200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:108210000-108212400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:108210000-108212600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:108210000-108212600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:108210000-108212600	Active TSS	NHLF	lung
9	chr9:108210200-108212200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:108210400-108212200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:108210400-108212200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:108210800-108212400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:108211000-108212200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:108211000-108212200	Flanking Active TSS	HUVEC	blood vessel
15	chr9:108211000-108212600	Active TSS	Brain Germinal Matrix	brain
16	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:108211200-108212200	Active TSS	Duodenum Mucosa	Duodenum
18	chr9:108211200-108212200	Active TSS	Stomach Smooth Muscle	stomach
19	chr9:108211200-108212200	Flanking Active TSS	Hela-S3	cervix
20	chr9:108211200-108212600	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr9:108211200-108213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:108211200-108214200	Weak transcription	Small Intestine	intestine
23	chr9:108211200-108219800	Weak transcription	Lung	lung
24	chr9:108211200-108220000	Weak transcription	Left Ventricle	heart
25	chr9:108211200-108220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:108211200-108220400	Weak transcription	Primary B cells from cord blood	blood
27	chr9:108211200-108220600	Weak transcription	Ovary	ovary
28	chr9:108211400-108212200	Enhancers	Colon Smooth Muscle	Colon
29	chr9:108211400-108212200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr9:108211400-108212200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr9:108211400-108212200	Flanking Active TSS	NHEK	skin
32	chr9:108211400-108212400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr9:108211400-108212600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:108211400-108212800	Active TSS	GM12878-XiMat	blood
35	chr9:108211400-108213000	Enhancers	Brain Cingulate Gyrus	brain
36	chr9:108211400-108213000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:108211400-108220000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr9:108211400-108220000	Weak transcription	Right Ventricle	heart
39	chr9:108211400-108222000	Weak transcription	Stomach Mucosa	stomach
40	chr9:108211600-108212200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:108211600-108212200	Enhancers	Fetal Intestine Small	intestine
42	chr9:108211600-108212200	Enhancers	Rectal Smooth Muscle	rectum
43	chr9:108211600-108212200	Enhancers	HSMM	muscle
44	chr9:108211600-108212600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:108211600-108212600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr9:108211600-108212600	Enhancers	Fetal Lung	lung
47	chr9:108211600-108219600	Weak transcription	Brain Substantia Nigra	brain
48	chr9:108211600-108220000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:108211800-108212200	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr9:108211800-108212200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links