Variant report

Variant	rs9649529
Chromosome Location	chr7:80172777-80172778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10233710	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10246970	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10282644	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1093829	0.84[ASN][1000 genomes]
rs1093830	0.84[ASN][1000 genomes]
rs1093831	0.88[ASN][1000 genomes]
rs1093833	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1093834	0.84[ASN][1000 genomes]
rs1093835	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11764390	0.81[EUR][1000 genomes]
rs1194195	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1194196	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1194197	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12155030	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12671075	0.84[EUR][1000 genomes]
rs1320408	0.82[ASN][1000 genomes]
rs1404312	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464793	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1761645	0.82[ASN][1000 genomes]
rs1761646	0.82[ASN][1000 genomes]
rs1851934	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1851935	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931694	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177616	0.86[EUR][1000 genomes]
rs2366739	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2781841	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28851188	0.86[EUR][1000 genomes]
rs28854232	0.86[EUR][1000 genomes]
rs4731606	0.86[EUR][1000 genomes]
rs6467251	0.83[ASN][1000 genomes]
rs701269	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71531176	0.83[ASN][1000 genomes]
rs71531177	0.86[EUR][1000 genomes]
rs7779873	0.86[EUR][1000 genomes]
rs7786174	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790259	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793698	0.82[ASN][1000 genomes]
rs7794010	0.82[ASN][1000 genomes]
rs7810280	0.82[ASN][1000 genomes]
rs819443	0.83[ASN][1000 genomes]
rs819445	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs819455	0.85[ASN][1000 genomes]
rs819457	0.85[ASN][1000 genomes]
rs819460	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs940542	0.82[ASN][1000 genomes]
rs9649527	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9649532	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429785	chr7:79589749-80177049	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1030961	chr7:80032525-80197468	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv538991	chr7:80032525-80197468	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv949205	chr7:80039695-80211200	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv888524	chr7:80107798-80723062	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv831043	chr7:80119414-80322092	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv948605	chr7:80119690-80298887	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1020682	chr7:80120651-80297697	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv888525	chr7:80148668-80232471	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9649529	ARX	trans	parietal	SCAN
rs9649529	CD36	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80168000-80181800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:80169800-80172800	Enhancers	NHDF-Ad	bronchial
3	chr7:80170000-80172800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:80170000-80172800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:80170200-80173800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:80171000-80172800	Enhancers	Osteobl	bone
7	chr7:80172200-80173000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:80172200-80173200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:80172600-80173200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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