Variant report

Variant	rs16889853
Chromosome Location	chr5:58741491-58741492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58737750..58739829-chr5:58740466..58743523,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1120303	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1156028	0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs12518641	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs1457112	0.80[ASN][1000 genomes]
rs1551564	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs16877169	0.82[TSI][hapmap]
rs16889865	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16889869	0.92[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs16889892	0.81[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs174039	0.94[CHB][hapmap];0.87[JPT][hapmap];0.94[YRI][hapmap];0.84[ASN][1000 genomes]
rs17795692	0.82[TSI][hapmap]
rs1824154	0.88[GIH][hapmap]
rs1902610	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2081092	0.88[GIH][hapmap]
rs2112910	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs28505532	0.80[ASN][1000 genomes]
rs28666954	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28729916	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35450986	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3852147	0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs41447947	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56173502	0.95[EUR][1000 genomes]
rs56349317	0.91[EUR][1000 genomes]
rs58232524	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59152084	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59246284	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60509830	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6870632	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs6871710	0.92[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs73097356	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7704141	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711639	0.84[GIH][hapmap]
rs7737908	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs988827	0.96[ASN][1000 genomes]
rs988828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][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	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv881705	chr5:58668669-58745872	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1034656	chr5:58674724-58755580	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv598253	chr5:58675538-58754510	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv881707	chr5:58741491-58784102	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16889853	C5orf35	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58705600-58751400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58709800-58756800	Weak transcription	Aorta	Aorta
3	chr5:58716000-58756600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:58731800-58764800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:58735800-58756400	Weak transcription	Psoas Muscle	Psoas
6	chr5:58736600-58744800	Enhancers	Fetal Brain Male	brain
7	chr5:58739000-58742200	Weak transcription	Fetal Lung	lung
8	chr5:58739400-58742200	Weak transcription	A549	lung
9	chr5:58740400-58751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:58741400-58746000	Enhancers	Fetal Brain Female	brain

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