Variant report

Variant	rs3132674
Chromosome Location	chr6:30202429-30202430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:30202175-30202436	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:30202105-30202468	MCF10A-Er-Src	breast:	n/a	n/a
3	BATF	chr6:30202214-30202520	GM12878	blood:	n/a	n/a
4	FOS	chr6:30202145-30202513	MCF10A-Er-Src	breast:	n/a	n/a
5	MEF2A	chr6:30202253-30202584	GM12878	blood:	n/a	chr6:30202505-30202519

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30200513..30202643-chr6:30293738..30295917,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM26-2	chr6:30201166-30203164	ucscGeneNc_uc003npj_2

Variant related genes	Relation type
TRIM26BP	TF binding region
HCG17	TF binding region
ENSG00000231074	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000270604	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1362089	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1573295	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2021365	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2021366	0.89[ASN][1000 genomes]
rs2074472	0.93[ASN][1000 genomes]
rs2074473	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2097772	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2106070	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2106071	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107196	0.87[ASN][1000 genomes]
rs2158283	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2253163	0.89[ASN][1000 genomes]
rs2253164	0.89[ASN][1000 genomes]
rs2284164	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285801	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2285802	0.83[EUR][1000 genomes]
rs2394737	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2394778	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2428503	0.80[AFR][1000 genomes]
rs2428505	0.83[EUR][1000 genomes]
rs2508029	0.89[ASN][1000 genomes]
rs2516723	0.83[EUR][1000 genomes]
rs2517611	0.80[AFR][1000 genomes]
rs2517614	0.83[AFR][1000 genomes]
rs2523713	0.80[AFR][1000 genomes]
rs2523722	0.83[AFR][1000 genomes]
rs28398051	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28441239	0.83[ASN][1000 genomes]
rs2844767	0.83[EUR][1000 genomes]
rs2844768	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2844778	0.85[ASN][1000 genomes]
rs2844782	0.89[ASN][1000 genomes]
rs2844786	0.89[ASN][1000 genomes]
rs3094130	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3094131	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3094132	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3094139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3094140	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3094614	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094615	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094635	0.83[EUR][1000 genomes]
rs3094636	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3094637	0.84[ASN][1000 genomes]
rs3094638	0.83[ASN][1000 genomes]
rs3094639	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129694	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130381	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130382	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130383	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130384	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130386	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130387	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3130388	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130391	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130393	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130394	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3132664	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3132665	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3132668	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3132669	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132671	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3132672	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35848695	0.87[ASN][1000 genomes]
rs4959046	0.89[ASN][1000 genomes]
rs6457164	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6457165	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6457167	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs718254	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7382110	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7383511	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs757257	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs765977	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7763162	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764012	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7774730	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs885914	0.96[ASN][1000 genomes]
rs885915	0.98[ASN][1000 genomes]
rs916568	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs916571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs916572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9261539	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261543	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261546	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261592	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs971570	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv884058	chr6:30182395-30202429	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv884060	chr6:30190640-30203602	Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3132674	GRM4	cis	cerebellum	SCAN
rs3132674	ZKSCAN3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30201400-30203000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:30202000-30202600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr6:30202000-30202600	Flanking Active TSS	Fetal Lung	lung
4	chr6:30202200-30202600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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