Variant report

Variant	rs6559659
Chromosome Location	chr9:84982792-84982793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10117890	0.89[ASN][1000 genomes]
rs10123309	0.89[ASN][1000 genomes]
rs10780541	0.83[ASN][1000 genomes]
rs10867832	0.83[ASN][1000 genomes]
rs10867834	0.83[ASN][1000 genomes]
rs10867835	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10867836	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10867837	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10867839	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10867840	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10867844	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11139538	0.91[ASN][1000 genomes]
rs11139554	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11794308	0.89[ASN][1000 genomes]
rs1330834	0.93[ASN][1000 genomes]
rs1411668	0.95[ASN][1000 genomes]
rs1888327	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1890344	0.89[ASN][1000 genomes]
rs1929097	0.93[ASN][1000 genomes]
rs1933577	0.93[ASN][1000 genomes]
rs1933580	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1933582	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1933583	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1933584	0.93[ASN][1000 genomes]
rs1933586	0.93[ASN][1000 genomes]
rs2038995	0.82[ASN][1000 genomes]
rs2767709	0.82[ASN][1000 genomes]
rs2788106	0.93[ASN][1000 genomes]
rs2788107	0.92[ASN][1000 genomes]
rs2788110	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2788112	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2788113	0.84[AMR][1000 genomes]
rs2993516	0.93[ASN][1000 genomes]
rs35064221	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4263847	0.92[ASN][1000 genomes]
rs4276765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4338186	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4489388	0.82[ASN][1000 genomes]
rs4563967	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4877229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877231	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4877691	0.95[ASN][1000 genomes]
rs6559656	0.85[ASN][1000 genomes]
rs7020546	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021352	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7027988	0.85[ASN][1000 genomes]
rs7047870	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7848262	0.95[ASN][1000 genomes]
rs7848263	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848823	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849168	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7852603	0.94[ASN][1000 genomes]
rs7857885	0.93[ASN][1000 genomes]
rs7859164	0.92[ASN][1000 genomes]
rs7859493	0.92[ASN][1000 genomes]
rs7861490	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893507	chr9:84799537-85097651	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893508	chr9:84954592-85080395	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893509	chr9:84954592-85097651	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893510	chr9:84954592-85117420	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6559659	C9orf64	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:84980800-84983000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:84981200-84982800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:84982000-84985600	Enhancers	Liver	Liver
4	chr9:84982200-84983800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:84982600-84983800	Weak transcription	Rectal Mucosa Donor 29	rectum

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