Variant report

Variant	rs17009509
Chromosome Location	chr4:126273929-126273930
allele	G/T
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:28)

rs_ID	r²[population]
rs12511204	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1354710	1.00[YRI][hapmap]
rs1355161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396686	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1533037	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1567047	1.00[YRI][hapmap]
rs17009511	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009520	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009526	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17009535	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009848	1.00[YRI][hapmap]
rs2068148	1.00[YRI][hapmap]
rs2710544	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710545	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710557	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710562	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710563	0.80[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710591	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2940780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56995730	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57565770	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57945315	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58972262	1.00[EUR][1000 genomes]
rs6830885	1.00[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840704	1.00[EUR][1000 genomes]
rs885271	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs970289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126242800-126279600	Weak transcription	Left Ventricle	heart
2	chr4:126254000-126274000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:126265200-126281200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:126266400-126279200	Weak transcription	Fetal Lung	lung
5	chr4:126268200-126275800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:126268200-126278600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:126268200-126279400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:126271800-126276600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:126271800-126277200	Weak transcription	Brain Angular Gyrus	brain
10	chr4:126272800-126278800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:126272800-126280800	Weak transcription	NHDF-Ad	bronchial
12	chr4:126273600-126274000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:126273600-126274000	Enhancers	Aorta	Aorta
14	chr4:126273600-126274200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:126273600-126274200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:126273600-126274200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr4:126273600-126274200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:126273600-126274200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr4:126273600-126274600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:126273800-126274000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:126273800-126274000	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr4:126273800-126274000	Active TSS	Brain Substantia Nigra	brain
23	chr4:126273800-126274000	Enhancers	Fetal Brain Male	brain
24	chr4:126273800-126274000	Enhancers	Fetal Stomach	stomach
25	chr4:126273800-126274200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:126273800-126274200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:126273800-126274200	Active TSS	Brain Anterior Caudate	brain
28	chr4:126273800-126274200	Active TSS	Brain Cingulate Gyrus	brain
29	chr4:126273800-126274200	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:126273800-126274200	Enhancers	Rectal Smooth Muscle	rectum
31	chr4:126273800-126274400	Enhancers	Colon Smooth Muscle	Colon
32	chr4:126273800-126274600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr4:126273800-126274800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links