Variant report

Variant	rs17379082
Chromosome Location	chr1:77812803-77812804
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	chr1:77808952..77811153-chr1:77811889..77814837,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12128049	0.81[TSI][hapmap]
rs12135900	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17098226	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17100231	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17100241	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17100274	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17100364	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17100436	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1823837	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034708	0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4033040	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4556409	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61783073	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17379082	RABGGTB	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77788800-77813000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:77789000-77813000	Weak transcription	NHLF	lung
3	chr1:77789000-77831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:77795000-77836400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:77800800-77813400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:77801000-77825800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:77803600-77813400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:77807000-77813000	Weak transcription	Brain Substantia Nigra	brain
10	chr1:77807600-77813000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:77808800-77813600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:77809000-77819200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:77809200-77813000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:77809200-77814400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:77811600-77814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:77811600-77815000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:77812400-77813600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:77812400-77813600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:77812400-77815600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:77812600-77813000	Enhancers	A549	lung
21	chr1:77812600-77813800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr1:77812800-77813000	Weak transcription	NHDF-Ad	bronchial
23	chr1:77812800-77813600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:77812800-77813600	Enhancers	HSMM	muscle
25	chr1:77812800-77813800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:77812800-77813800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:77812800-77814400	Enhancers	Primary T cells from cord blood	blood
28	chr1:77812800-77814600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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