Variant report

Variant	rs17079813
Chromosome Location	chr5:179366824-179366825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D9B-3	chr5:179366457-179367132	NONHSAT105659

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10078686	1.00[MEX][hapmap]
rs12520005	1.00[AMR][1000 genomes]
rs12521533	1.00[AMR][1000 genomes]
rs17079679	1.00[MEX][hapmap]
rs17079857	0.86[AFR][1000 genomes]
rs269459	1.00[MEX][hapmap]
rs272440	1.00[MEX][hapmap]
rs28578757	1.00[AMR][1000 genomes]
rs34823714	1.00[AMR][1000 genomes]
rs58493575	1.00[AMR][1000 genomes]
rs58548426	1.00[AMR][1000 genomes]
rs73335521	1.00[AMR][1000 genomes]
rs73338298	1.00[AMR][1000 genomes]
rs73342216	1.00[AMR][1000 genomes]
rs73342221	0.91[AFR][1000 genomes]
rs73342292	0.91[AFR][1000 genomes]
rs73344340	1.00[AMR][1000 genomes]
rs73348275	1.00[AMR][1000 genomes]
rs73350175	1.00[AMR][1000 genomes]
rs73810998	1.00[AMR][1000 genomes]
rs7717213	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	153 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179344600-179381600	Weak transcription	Fetal Brain Male	brain
2	chr5:179347200-179381000	Weak transcription	Brain Angular Gyrus	brain
3	chr5:179347400-179372000	Weak transcription	Brain Germinal Matrix	brain
4	chr5:179351000-179372200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:179354200-179381400	Weak transcription	Fetal Brain Female	brain
6	chr5:179359000-179368800	Weak transcription	Right Atrium	heart
7	chr5:179359000-179381000	Weak transcription	Brain Substantia Nigra	brain
8	chr5:179359000-179381200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:179359400-179373000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:179360200-179377400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:179361200-179372200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:179363000-179368200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:179363400-179373800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:179364600-179368200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:179366600-179372200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:179366600-179382000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links