Variant report

Variant	rs171630
Chromosome Location	chr5:89889392-89889393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10064606	0.85[EUR][1000 genomes]
rs11958484	0.85[EUR][1000 genomes]
rs149321	0.81[ASN][1000 genomes]
rs154566	0.82[ASN][1000 genomes]
rs2366775	0.80[ASN][1000 genomes]
rs250366	0.82[ASN][1000 genomes]
rs250369	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27196	0.81[ASN][1000 genomes]
rs27197	0.81[ASN][1000 genomes]
rs28480058	0.80[ASN][1000 genomes]
rs4916808	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs567441	0.81[ASN][1000 genomes]
rs62375083	0.80[EUR][1000 genomes]
rs62375094	0.84[EUR][1000 genomes]
rs656679	0.82[ASN][1000 genomes]
rs6861067	0.82[EUR][1000 genomes]
rs6891287	0.81[ASN][1000 genomes]
rs6891840	0.80[ASN][1000 genomes]
rs9283789	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9293549	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs171630	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89884600-89890400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:89886600-89891000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:89887400-89890200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr5:89888600-89897400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:89889200-89889800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links