Variant report

Variant	rs427557
Chromosome Location	chr7:65519250-65519251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1144894	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1144895	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1167385	0.86[AFR][1000 genomes]
rs1167386	0.85[AFR][1000 genomes]
rs1167411	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1167612	0.82[AMR][1000 genomes]
rs1182882	0.81[EUR][1000 genomes]
rs1183245	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11971949	0.81[AMR][1000 genomes]
rs13247295	0.83[AMR][1000 genomes]
rs160635	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2220626	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2949696	0.83[AMR][1000 genomes]
rs313804	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs427575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432667	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs448725	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6957690	0.81[AMR][1000 genomes]
rs6961717	0.81[AMR][1000 genomes]
rs697968	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs697969	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs697970	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs780742	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs780743	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs780744	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs780998	0.84[AMR][1000 genomes]
rs809080	0.83[AMR][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs427557	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs427557	RNU6-96P	cis	Thyroid	GTEx
rs427557	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs427557	RP4-756H11.3	cis	lung	GTEx
rs427557	GS1-124K5.4	cis	Stomach	GTEx
rs427557	RP4-756H11.3	cis	Thyroid	GTEx
rs427557	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs427557	GS1-124K5.4	cis	Artery Aorta	GTEx
rs427557	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs427557	GTF2IRD1P1	cis	Thyroid	GTEx
rs427557	RP4-756H11.3	cis	Artery Tibial	GTEx
rs427557	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs427557	GS1-124K5.4	cis	Whole Blood	GTEx
rs427557	RP4-756H11.3	cis	Artery Aorta	GTEx
rs427557	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs427557	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs427557	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs427557	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65516000-65520800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:65516400-65520000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:65516400-65520000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:65516400-65520400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:65516600-65520000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:65516600-65520200	Weak transcription	Osteobl	bone
7	chr7:65516600-65520400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:65517200-65520200	Enhancers	GM12878-XiMat	blood
9	chr7:65517400-65520400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:65517400-65520800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:65517800-65520200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:65518400-65519400	Weak transcription	NHDF-Ad	bronchial
13	chr7:65518400-65519400	Weak transcription	NHEK	skin
14	chr7:65518800-65520200	Weak transcription	NH-A	brain
15	chr7:65519000-65519400	Enhancers	Spleen	Spleen
16	chr7:65519200-65520200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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