Variant report

Variant	rs6794214
Chromosome Location	chr3:155110950-155110951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11706749	0.90[EUR][1000 genomes]
rs11713552	0.94[EUR][1000 genomes]
rs11715278	0.88[JPT][hapmap]
rs12487150	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12493778	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs12496803	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13066178	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs13081656	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs13083852	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap]
rs35424673	0.95[EUR][1000 genomes]
rs4345113	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs4630984	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4680171	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680172	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.97[TSI][hapmap]
rs4680173	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680174	0.85[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs4680175	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4680176	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4680177	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes]
rs6440985	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs6762452	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6807784	0.85[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs6807961	0.85[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs7612603	0.81[EUR][1000 genomes]
rs7619730	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7627097	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs9841365	0.84[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[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	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6794214	GFM1	cis	cerebellum	SCAN
rs6794214	BRD7	cis	parietal	SCAN
rs6794214	SLC33A1	cis	cerebellum	SCAN
rs6794214	PLCH1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155105600-155114400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:155110000-155111400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:155110400-155111400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:155110600-155111000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:155110600-155111200	Weak transcription	HMEC	breast

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