Variant report

Variant	rs62375083
Chromosome Location	chr5:89955691-89955692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89954656..89958322-chr5:89963130..89966390,3	K562	blood:
2	chr5:89765764..89769852-chr5:89955166..89959028,3	K562	blood:
3	chr5:89950925..89957089-chr5:90674771..90680308,6	K562	blood:
4	chr5:89954358..89956841-chr5:89967131..89969793,2	K562	blood:
5	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
6	chr5:89702933..89707555-chr5:89951683..89956853,5	K562	blood:

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10035335	0.81[EUR][1000 genomes]
rs10037067	0.81[EUR][1000 genomes]
rs10040165	0.82[EUR][1000 genomes]
rs10043564	0.92[ASN][1000 genomes]
rs10064606	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11958484	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12186867	0.92[ASN][1000 genomes]
rs16868980	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16876822	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs171630	0.80[EUR][1000 genomes]
rs2366926	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs250369	0.81[EUR][1000 genomes]
rs28796004	0.82[EUR][1000 genomes]
rs4916683	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4916685	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4916808	0.88[EUR][1000 genomes]
rs55835641	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56255871	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62375094	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62375106	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6880239	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7716829	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs908818	0.91[ASN][1000 genomes]
rs9283789	0.83[EUR][1000 genomes]
rs9293549	0.84[EUR][1000 genomes]
rs970319	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1029970	chr5:89940489-89986831	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv1032225	chr5:89940489-89999954	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1025391	chr5:89943364-89995164	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv537805	chr5:89943364-89995164	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62375083	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:89941400-89957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:89941800-89957600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:89944800-89956600	Weak transcription	Fetal Brain Male	brain
5	chr5:89948000-89955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:89949600-89964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:89950200-89981600	Weak transcription	Fetal Brain Female	brain
8	chr5:89950400-89956600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:89950800-89964000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:89950800-89973800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:89951800-89956200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:89952400-89957200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:89954800-89972600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:89955200-89957400	Active TSS	K562	blood
16	chr5:89955400-89956800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:89955400-89964000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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