Variant report

Variant	rs1353749
Chromosome Location	chr5:58379309-58379310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10037973	0.94[JPT][hapmap]
rs10038704	0.94[JPT][hapmap]
rs10061553	0.81[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs10075104	0.81[JPT][hapmap]
rs11739293	0.92[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11958928	0.82[JPT][hapmap]
rs12654005	0.88[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs13178315	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1363882	0.94[JPT][hapmap]
rs1391649	0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1391650	0.94[JPT][hapmap]
rs1391651	0.94[JPT][hapmap];0.81[LWK][hapmap]
rs28555377	0.93[EUR][1000 genomes]
rs2910642	0.92[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2968009	0.81[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs5010782	0.81[JPT][hapmap]
rs6898374	0.94[JPT][hapmap]
rs929820	0.87[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1353749	C5orf35	cis	cerebellum	SCAN
rs1353749	RAB3C	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58376400-58388200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:58376400-58389200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58376400-58390400	Weak transcription	Hela-S3	cervix
4	chr5:58376600-58386200	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:58376600-58387000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:58376800-58385800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:58378000-58380000	Genic enhancers	A549	lung
8	chr5:58378200-58391800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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