Variant report

Variant	rs4775178
Chromosome Location	chr15:59855406-59855407
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10438334	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12443333	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12902469	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28405302	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28490567	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35634961	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3935730	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3935731	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4775187	0.91[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4775188	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55853439	0.91[EUR][1000 genomes]
rs58735029	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6494119	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176261	0.91[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7176837	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7176947	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920277	0.91[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4775178	GCOM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59841600-59861600	Weak transcription	Gastric	stomach
2	chr15:59848800-59857600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:59851000-59859000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:59853600-59855600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr15:59853800-59861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:59855000-59858800	Weak transcription	Hela-S3	cervix

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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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