Variant report

Variant	rs2444009
Chromosome Location	chr15:45054952-45054953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45003593..45005098-chr15:45054894..45057057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166710	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1060392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1295358	0.85[CEU][hapmap];0.97[GIH][hapmap]
rs14711	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1901534	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1901535	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1901537	0.83[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs2084835	0.80[MEX][hapmap];0.80[AMR][1000 genomes]
rs2123149	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2254831	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2254835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2290331	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2443976	0.95[EUR][1000 genomes]
rs2444003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2444010	0.96[EUR][1000 genomes]
rs2468064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs2468074	0.97[EUR][1000 genomes]
rs2468075	0.95[EUR][1000 genomes]
rs2468077	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs2470914	0.97[EUR][1000 genomes]
rs3100139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3100142	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3110172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3110173	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3110174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3110176	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3110182	0.96[EUR][1000 genomes]
rs3110662	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3110675	0.95[EUR][1000 genomes]
rs6493108	0.83[EUR][1000 genomes]
rs6493109	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs7165535	0.80[MEX][hapmap]
rs7168090	0.84[JPT][hapmap]
rs7172083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs935886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2444009	TRIM69	cis	Artery Tibial	GTEx
rs2444009	TRIM69	cis	Esophagus Muscularis	GTEx
rs2444009	TRIM69	cis	cerebellum	SCAN
rs2444009	TRIM69	cis	Frontal Cortex	GTEx
rs2444009	METT5D1	trans	lymphoblastoid	seeQTL
rs2444009	CHST14	cis	parietal	SCAN
rs2444009	CHP	cis	cerebellum	SCAN
rs2444009	TRIM69	cis	Adipose Subcutaneous	GTEx
rs2444009	TRIM69	cis	Muscle Skeletal	GTEx
rs2444009	TRIM69	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45046400-45062200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr15:45047600-45059600	Weak transcription	GM12878-XiMat	blood
3	chr15:45047600-45076000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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