Variant report

Variant	rs3820579
Chromosome Location	chr1:57489529-57489530
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11206942	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11206954	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11206955	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206958	0.90[ASN][1000 genomes]
rs11206961	0.85[ASN][1000 genomes]
rs11206962	0.82[ASN][1000 genomes]
rs11589281	0.85[ASN][1000 genomes]
rs11810899	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035887	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12036280	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12062362	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082861	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118564	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144161	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329448	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329451	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17114695	0.90[AMR][1000 genomes]
rs17114816	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1831871	0.93[ASN][1000 genomes]
rs1854508	0.99[ASN][1000 genomes]
rs2026083	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754268	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768200	0.87[ASN][1000 genomes]
rs3768201	0.90[ASN][1000 genomes]
rs3768202	0.90[ASN][1000 genomes]
rs3768203	0.90[ASN][1000 genomes]
rs3768204	0.90[ASN][1000 genomes]
rs3768205	0.90[ASN][1000 genomes]
rs3768206	0.90[ASN][1000 genomes]
rs3768209	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768211	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820578	0.87[ASN][1000 genomes]
rs3820581	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4912233	0.90[ASN][1000 genomes]
rs4912420	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4912422	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4912423	0.89[ASN][1000 genomes]
rs6668180	0.85[ASN][1000 genomes]
rs6668269	0.99[ASN][1000 genomes]
rs6676740	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6679906	1.00[ASN][1000 genomes]
rs6681325	0.88[ASN][1000 genomes]
rs697580	0.97[ASN][1000 genomes]
rs706353	1.00[ASN][1000 genomes]
rs706357	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs706360	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706361	0.85[AMR][1000 genomes]
rs706364	0.90[ASN][1000 genomes]
rs72917455	0.90[ASN][1000 genomes]
rs7533953	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs835447	0.90[ASN][1000 genomes]
rs944923	0.99[ASN][1000 genomes]
rs952703	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57474200-57490200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:57477600-57490200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:57481600-57490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:57483200-57494000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57483400-57490400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:57483400-57490600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:57483600-57490600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:57485200-57494800	Weak transcription	Fetal Brain Female	brain
9	chr1:57485400-57489600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:57485400-57490600	Weak transcription	HepG2	liver
11	chr1:57485400-57498000	Weak transcription	Liver	Liver
12	chr1:57486000-57502600	Weak transcription	Fetal Brain Male	brain
13	chr1:57486800-57490400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:57487800-57498800	Weak transcription	Fetal Intestine Large	intestine
15	chr1:57489200-57489600	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links