Variant report

Variant	rs656679
Chromosome Location	chr5:89879259-89879260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89855529..89859468-chr5:89877001..89881365,3	MCF-7	breast:
2	chr5:89878566..89881386-chr5:89882333..89884727,3	K562	blood:
3	chr5:89878566..89881617-chr5:89882501..89884794,5	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10043564	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10064606	0.83[JPT][hapmap]
rs11958484	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs12186867	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs12653924	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1316970	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs149321	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs154566	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154569	0.86[JPT][hapmap]
rs1673381	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs171630	0.82[ASN][1000 genomes]
rs2366772	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2366775	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs250366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250369	0.96[ASN][1000 genomes]
rs250377	0.82[JPT][hapmap]
rs257847	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs27196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27197	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]
rs27201	0.81[JPT][hapmap]
rs28480058	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112773	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs42467	0.86[JPT][hapmap]
rs4588621	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[ASN][1000 genomes]
rs5028525	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs511393	0.81[JPT][hapmap]
rs567441	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599432	1.00[JPT][hapmap]
rs649449	0.83[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6891287	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6891840	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6892132	0.83[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs908818	0.82[JPT][hapmap]
rs9283789	0.86[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	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs656679	GPR98	cis	cerebellum	SCAN
rs656679	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs656679	GPR98	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89859400-89884200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:89867400-89889200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:89868800-89884400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:89869200-89881200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:89872000-89881600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:89876400-89881000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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