Variant report

Variant	rs2239550
Chromosome Location	chr3:52822509-52822510
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1014969	0.82[EUR][1000 genomes]
rs1029871	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1042779	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1075653	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076425	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780035	0.81[AMR][1000 genomes]
rs11130323	0.81[EUR][1000 genomes]
rs11130325	0.81[EUR][1000 genomes]
rs11130327	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11717836	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12497998	0.84[EUR][1000 genomes]
rs13061423	0.87[EUR][1000 genomes]
rs13071584	0.86[EUR][1000 genomes]
rs13082208	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13082960	0.83[EUR][1000 genomes]
rs13087772	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13095332	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2019065	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2071506	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071507	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071508	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2230534	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2230535	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2239549	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239551	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239699	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240919	0.92[ASN][1000 genomes]
rs2240920	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268023	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268024	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2268025	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2268026	0.82[EUR][1000 genomes]
rs2268027	0.81[AMR][1000 genomes]
rs2270197	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284350	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284351	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286798	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286800	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2300149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302417	0.81[ASN][1000 genomes]
rs2336545	0.86[EUR][1000 genomes]
rs2535629	0.80[ASN][1000 genomes]
rs2710323	0.86[ASN][1000 genomes]
rs2710331	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774354	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774355	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687549	0.81[AMR][1000 genomes]
rs4687551	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687552	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687648	0.82[EUR][1000 genomes]
rs4687650	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687654	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255396	0.82[EUR][1000 genomes]
rs6778329	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs678	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792369	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6976	0.80[AMR][1000 genomes]
rs736408	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs746694	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8906	0.80[AMR][1000 genomes]
rs9324	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881468	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998909	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2239550	MUSTN1	cis	Artery Aorta	GTEx
rs2239550	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs2239550	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2239550	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs2239550	PBRM1	cis	Thyroid	GTEx
rs2239550	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52805600-52825800	Weak transcription	Right Ventricle	heart
2	chr3:52814800-52826400	Genic enhancers	Liver	Liver
3	chr3:52816400-52825800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:52819600-52823000	Weak transcription	Spleen	Spleen
5	chr3:52820400-52822600	Flanking Active TSS	HepG2	liver
6	chr3:52822000-52824000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:52822400-52822600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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