Variant report

Variant	rs27197
Chromosome Location	chr5:89894564-89894565
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89768356..89770490-chr5:89893117..89895355,2	MCF-7	breast:
2	chr5:89893486..89895205-chr5:89895612..89897548,2	K562	blood:

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10043564	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs10064606	0.83[JPT][hapmap]
rs11958484	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs12186867	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12653924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1316970	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1474119	0.96[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs149321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154566	0.97[ASN][1000 genomes]
rs154569	0.86[JPT][hapmap]
rs1673381	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs171630	0.81[ASN][1000 genomes]
rs2366772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2366775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs250366	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs250369	0.96[ASN][1000 genomes]
rs250377	0.82[JPT][hapmap]
rs257847	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs27196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs27201	0.81[JPT][hapmap]
rs28480058	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3112773	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42467	0.86[JPT][hapmap]
rs4588621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5028525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511393	0.81[JPT][hapmap]
rs567441	0.92[ASN][1000 genomes]
rs599432	1.00[JPT][hapmap]
rs649449	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs656679	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs6891287	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6891840	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6892132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs908818	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9283789	0.89[ASN][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
rs27197	GPR98	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89888600-89897400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:89892800-89909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:89893000-89907800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:89893200-89902000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:89893400-89894600	Enhancers	Brain Cingulate Gyrus	brain
6	chr5:89894000-89894600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:89894200-89894600	Enhancers	Brain Angular Gyrus	brain
8	chr5:89894200-89894600	Active TSS	Brain Germinal Matrix	brain
9	chr5:89894200-89894600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
10	chr5:89894200-89894600	Enhancers	Brain Substantia Nigra	brain
11	chr5:89894200-89894600	Enhancers	Fetal Brain Male	brain
12	chr5:89894200-89894800	Flanking Active TSS	Fetal Brain Female	brain
13	chr5:89894400-89894600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr5:89894400-89894800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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