Variant report

Variant	rs1540651
Chromosome Location	chr7:65650121-65650122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65649367..65652359-chr7:65653960..65655617,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10215948	0.81[EUR][1000 genomes]
rs10240249	0.86[AFR][1000 genomes]
rs10253922	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10256544	0.82[AMR][1000 genomes]
rs10257427	0.81[EUR][1000 genomes]
rs10267430	0.80[EUR][1000 genomes]
rs10271553	0.82[AFR][1000 genomes]
rs1129531	0.88[AFR][1000 genomes]
rs1144894	0.83[AMR][1000 genomes]
rs1144895	0.82[AMR][1000 genomes]
rs1167390	0.82[AFR][1000 genomes]
rs1167395	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1167411	0.82[AMR][1000 genomes]
rs1167612	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1182882	0.84[AMR][1000 genomes]
rs1183245	0.83[AMR][1000 genomes]
rs11971949	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11974219	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11974264	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13225383	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13229046	0.87[ASN][1000 genomes]
rs13240492	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13245728	0.83[AFR][1000 genomes]
rs13247295	0.85[AMR][1000 genomes]
rs13309935	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1565531	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1612452	0.82[AFR][1000 genomes]
rs1976200	0.83[AFR][1000 genomes]
rs2087647	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2173570	0.81[EUR][1000 genomes]
rs2220626	0.85[AMR][1000 genomes]
rs2249458	0.81[AFR][1000 genomes]
rs2420168	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2420173	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2420174	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs28391294	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs28470208	0.82[AFR][1000 genomes]
rs28682868	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2949696	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35028832	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35034167	0.82[AFR][1000 genomes]
rs3935391	0.80[EUR][1000 genomes]
rs4368860	0.88[AFR][1000 genomes]
rs4718319	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs55748098	0.81[EUR][1000 genomes]
rs55962648	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57866200	0.81[AFR][1000 genomes]
rs59466412	0.81[AFR][1000 genomes]
rs6945843	0.81[EUR][1000 genomes]
rs6946143	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6957690	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6958484	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6960476	0.81[EUR][1000 genomes]
rs6961717	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6963646	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6967708	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6971509	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6977501	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs697968	0.81[AMR][1000 genomes]
rs697969	0.84[AMR][1000 genomes]
rs697970	0.85[AMR][1000 genomes]
rs7782806	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7786892	0.89[AFR][1000 genomes]
rs7801282	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780743	0.82[AMR][1000 genomes]
rs780744	0.82[AMR][1000 genomes]
rs7809814	0.88[AFR][1000 genomes]
rs780998	0.86[AMR][1000 genomes]
rs875971	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs880166	0.81[AMR][1000 genomes]
rs908915	0.88[AFR][1000 genomes]
rs937495	0.80[EUR][1000 genomes]
rs9969301	0.80[EUR][1000 genomes]
rs9986696	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	nsv971172	chr7:65616238-65653268	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1540651	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs1540651	GTF2IRD1P1	cis	Thyroid	GTEx
rs1540651	GS1-124K5.4	cis	Whole Blood	GTEx
rs1540651	RP4-756H11.3	cis	Thyroid	GTEx
rs1540651	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs1540651	RP4-756H11.3	cis	Artery Aorta	GTEx
rs1540651	RP4-756H11.3	cis	Artery Tibial	GTEx
rs1540651	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs1540651	GS1-124K5.4	cis	Artery Aorta	GTEx
rs1540651	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs1540651	GS1-124K5.11	cis	Thyroid	GTEx
rs1540651	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1540651	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs1540651	RP4-756H11.3	cis	lung	GTEx
rs1540651	RNU6-96P	cis	Thyroid	GTEx
rs1540651	GS1-124K5.4	cis	Stomach	GTEx
rs1540651	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs1540651	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65649200-65652200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:65649800-65652600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:65650000-65652400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:65650000-65652600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:65650000-65652600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:65650000-65652600	Weak transcription	NHDF-Ad	bronchial
7	chr7:65650000-65654600	Weak transcription	HepG2	liver

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