Variant report

Variant	rs626074
Chromosome Location	chr3:54658173-54658174
allele	G/T
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:17)

rs_ID	r²[population]
rs1366032	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs483200	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs495532	0.81[ASW][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4955988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs496625	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs499292	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs508907	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs551799	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs595040	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs595993	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs605284	0.96[CEU][hapmap]
rs616113	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs618669	0.80[AMR][1000 genomes]
rs661201	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs667612	0.92[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs670335	0.92[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs674542	0.85[AMR][1000 genomes];0.89[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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs626074	RFT1	cis	cerebellum	SCAN
rs626074	RRP9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:54652800-54665000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:54654800-54662400	Weak transcription	Right Atrium	heart
5	chr3:54655000-54662400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:54655600-54662800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:54657600-54658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:54657800-54659800	Weak transcription	Esophagus	oesophagus

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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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