Variant report

Variant	rs12001288
Chromosome Location	chr9:18478216-18478217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10119114	1.00[CEU][hapmap]
rs10511637	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10511658	0.81[YRI][hapmap]
rs1147795	1.00[CEU][hapmap]
rs11999281	0.80[YRI][hapmap]
rs12000949	0.87[YRI][hapmap]
rs12000950	0.87[YRI][hapmap]
rs12001790	0.87[YRI][hapmap]
rs12003118	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs12003267	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs12005242	0.81[YRI][hapmap]
rs13294727	0.82[YRI][hapmap]
rs1361533	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16936775	0.93[YRI][hapmap]
rs16936777	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16936780	0.86[YRI][hapmap]
rs16936815	0.86[YRI][hapmap]
rs1891042	1.00[CEU][hapmap]
rs1891043	1.00[CEU][hapmap]
rs60008508	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60561389	0.82[AFR][1000 genomes]
rs7019792	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs7044968	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18474200-18478800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:18474800-18478600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:18474800-18478800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:18474800-18480200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:18475000-18478600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:18475200-18478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:18475200-18484800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:18475400-18478600	Weak transcription	Aorta	Aorta
9	chr9:18475400-18479000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:18475400-18481600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:18475400-18482600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:18475800-18478600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:18476000-18485600	Weak transcription	Fetal Stomach	stomach
14	chr9:18476200-18479800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr9:18476600-18479000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:18476600-18479000	Enhancers	Fetal Heart	heart
17	chr9:18477000-18478800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr9:18477000-18479000	Enhancers	Brain Hippocampus Middle	brain
19	chr9:18477000-18479400	Flanking Active TSS	NH-A	brain
20	chr9:18477200-18478400	Enhancers	HSMMtube	muscle
21	chr9:18477200-18478600	Weak transcription	NHLF	lung
22	chr9:18477200-18478800	Flanking Active TSS	NHDF-Ad	bronchial
23	chr9:18477400-18479000	Enhancers	Brain Germinal Matrix	brain
24	chr9:18477400-18489200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:18477600-18478600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:18477600-18478600	Weak transcription	Brain Angular Gyrus	brain
27	chr9:18477600-18478800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr9:18477600-18481600	Weak transcription	HUVEC	blood vessel
29	chr9:18477800-18478400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:18477800-18478400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:18477800-18478800	Flanking Active TSS	Osteobl	bone
32	chr9:18478000-18479200	Flanking Active TSS	HSMM	muscle
33	chr9:18478200-18478400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:18478200-18478600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:18478200-18478800	Weak transcription	Brain Substantia Nigra	brain
36	chr9:18478200-18482800	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links