Variant report

Variant	rs17605653
Chromosome Location	chr5:126949223-126949224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1031847	0.93[EUR][1000 genomes]
rs11241933	0.82[AFR][1000 genomes]
rs11739013	0.90[AFR][1000 genomes]
rs11743384	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746839	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746912	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11950491	0.82[AFR][1000 genomes]
rs12188818	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13154759	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13164325	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13166202	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13182035	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13183092	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13190411	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34700780	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35111054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35376602	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851476	0.93[EUR][1000 genomes]
rs61573394	0.82[AFR][1000 genomes]
rs6595781	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67143037	1.00[ASN][1000 genomes]
rs6870347	0.94[EUR][1000 genomes]
rs6876031	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72794203	1.00[ASN][1000 genomes]
rs72794209	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337177	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723560	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv830479	chr5:126849254-127053121	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv519906	chr5:126943293-126955918	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17605653	CHSY3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126944200-126951400	Weak transcription	NHEK	skin
2	chr5:126944600-126951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:126944600-126960400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:126947600-126962000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:126948600-126951200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:126948800-126951600	Weak transcription	HMEC	breast
7	chr5:126949000-126951400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:126949000-126953800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:126949200-126952000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links