Variant report

Variant	rs1473351
Chromosome Location	chr3:67719113-67719114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10510966	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706254	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11716677	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718788	0.87[ASN][1000 genomes]
rs12714500	0.82[EUR][1000 genomes]
rs13060205	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13062710	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065696	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13068759	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13069212	0.82[EUR][1000 genomes]
rs13069251	0.82[EUR][1000 genomes]
rs13070332	0.82[EUR][1000 genomes]
rs13076100	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13077262	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13078350	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081838	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13083820	0.82[EUR][1000 genomes]
rs13087072	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13090197	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13091275	0.81[EUR][1000 genomes]
rs13091330	0.83[EUR][1000 genomes]
rs13094934	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13099253	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1376028	0.82[EUR][1000 genomes]
rs1376030	0.81[JPT][hapmap]
rs1563808	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814519	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1823476	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2167181	0.81[AMR][1000 genomes]
rs2198015	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2198016	0.82[EUR][1000 genomes]
rs2218796	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2235	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2362455	0.80[AMR][1000 genomes]
rs6548721	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6766403	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6770260	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6773969	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779395	0.82[EUR][1000 genomes]
rs6781799	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6786211	0.82[EUR][1000 genomes]
rs6788874	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6797460	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6798228	0.81[AMR][1000 genomes]
rs6806285	0.82[EUR][1000 genomes]
rs6806536	0.82[EUR][1000 genomes]
rs7434004	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7610446	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7615766	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7625814	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632886	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639427	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7640220	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647518	0.82[EUR][1000 genomes]
rs935734	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9824834	0.83[EUR][1000 genomes];0.84[ASN][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	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv428739	chr3:67656829-67730379	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1473351	RP11-81N13.1	cis	Thyroid	GTEx
rs1473351	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67705600-67756200	Weak transcription	Aorta	Aorta
2	chr3:67705800-67776000	Weak transcription	Ovary	ovary
3	chr3:67706400-67721000	Weak transcription	Left Ventricle	heart
4	chr3:67706800-67726600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:67706800-67727200	Weak transcription	A549	lung
6	chr3:67712200-67728400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:67716200-67724200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:67717200-67730800	Weak transcription	Gastric	stomach
9	chr3:67717400-67723600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:67717400-67724600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:67717400-67728200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:67717600-67728000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:67719000-67719200	ZNF genes & repeats	Primary T cells from cord blood	blood
14	chr3:67719000-67724400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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