Variant report

Variant	rs60562826
Chromosome Location	chr5:89958285-89958286
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	chr5:89702478..89704273-chr5:89957173..89959888,2	K562	blood:
4	chr5:89951486..89954210-chr5:89956379..89958966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10044044	0.81[AMR][1000 genomes]
rs10462488	0.82[AMR][1000 genomes]
rs10462489	0.81[AMR][1000 genomes]
rs10514331	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11951632	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11952742	0.82[AMR][1000 genomes]
rs11955565	0.87[ASN][1000 genomes]
rs11955749	0.82[AMR][1000 genomes]
rs11959270	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11960887	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1344030	0.82[AMR][1000 genomes]
rs154556	0.81[AMR][1000 genomes]
rs16868839	0.82[AMR][1000 genomes]
rs16868892	0.82[AMR][1000 genomes]
rs16868894	0.82[AMR][1000 genomes]
rs16868901	0.82[AMR][1000 genomes]
rs16868903	0.82[AMR][1000 genomes]
rs16868906	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16868924	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16868927	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16868932	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16868964	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16868970	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16868972	0.93[ASN][1000 genomes]
rs16868985	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16869013	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16869032	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16869043	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1878881	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1996551	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257848	0.82[AMR][1000 genomes]
rs41303352	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41308295	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45478296	0.82[AMR][1000 genomes]
rs45507696	0.82[AMR][1000 genomes]
rs4916680	0.81[AMR][1000 genomes]
rs4916803	0.82[AMR][1000 genomes]
rs4916804	0.82[AMR][1000 genomes]
rs4916805	0.82[AMR][1000 genomes]
rs4916807	0.82[AMR][1000 genomes]
rs4916809	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4916810	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs55720814	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55918113	0.82[AMR][1000 genomes]
rs56002033	0.81[AMR][1000 genomes]
rs56360530	0.82[AMR][1000 genomes]
rs57437217	0.82[AMR][1000 genomes]
rs58132310	0.82[AMR][1000 genomes]
rs58582125	0.94[ASN][1000 genomes]
rs59496152	0.82[AMR][1000 genomes]
rs60359999	0.82[AMR][1000 genomes]
rs60651883	0.82[AMR][1000 genomes]
rs61525440	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66977476	0.82[AMR][1000 genomes]
rs67556741	0.82[AMR][1000 genomes]
rs68045375	0.82[AMR][1000 genomes]
rs6867004	0.86[ASN][1000 genomes]
rs6875517	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6880570	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6889828	0.82[AMR][1000 genomes]
rs72656677	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73772469	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7701844	0.82[AMR][1000 genomes]
rs7707357	0.82[AMR][1000 genomes]
rs7709691	0.82[AMR][1000 genomes]
rs7721027	0.93[ASN][1000 genomes]
rs7729205	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7729644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9293546	0.81[AMR][1000 genomes]
rs950692	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 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	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:89949600-89964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:89950200-89981600	Weak transcription	Fetal Brain Female	brain
4	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:89950800-89964000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:89950800-89973800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:89954800-89972600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:89955400-89964000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:89955800-89964800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:89957600-89959200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:89957600-89964000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:89957600-89969400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:89957800-89965000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:89958000-89958400	Genic enhancers	K562	blood
15	chr5:89958200-89958400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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