Variant report

Variant	rs6460279
Chromosome Location	chr7:65662761-65662762
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	chr7:65662738..65664667-chr7:65666505..65668854,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1000464	0.88[EUR][1000 genomes]
rs10224872	0.90[EUR][1000 genomes]
rs10228885	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10240249	0.82[EUR][1000 genomes]
rs10240949	0.90[EUR][1000 genomes]
rs10250544	0.95[EUR][1000 genomes]
rs10253922	0.81[EUR][1000 genomes]
rs10255397	0.86[EUR][1000 genomes]
rs10256544	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10257911	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10260426	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10261398	0.90[EUR][1000 genomes]
rs10263690	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10272149	0.83[EUR][1000 genomes]
rs10276077	0.90[EUR][1000 genomes]
rs10282433	0.91[EUR][1000 genomes]
rs10447522	0.96[EUR][1000 genomes]
rs1083554	0.88[EUR][1000 genomes]
rs10950033	0.91[EUR][1000 genomes]
rs1129531	0.82[EUR][1000 genomes]
rs11760844	0.91[EUR][1000 genomes]
rs11769079	0.86[EUR][1000 genomes]
rs11984115	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12531677	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12534500	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537823	0.91[EUR][1000 genomes]
rs13225672	0.85[EUR][1000 genomes]
rs13230545	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13309935	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1532571	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1643375	0.81[EUR][1000 genomes]
rs1875057	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1983372	0.80[EUR][1000 genomes]
rs2036263	0.90[EUR][1000 genomes]
rs2088653	0.95[EUR][1000 genomes]
rs2088655	0.95[EUR][1000 genomes]
rs2420173	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2420174	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28391294	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28491091	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2901152	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2909688	0.93[EUR][1000 genomes]
rs34913718	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3893216	0.93[EUR][1000 genomes]
rs4078376	0.91[EUR][1000 genomes]
rs4149461	0.91[EUR][1000 genomes]
rs4236208	0.91[EUR][1000 genomes]
rs4587224	0.91[EUR][1000 genomes]
rs4718319	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4718324	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718328	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4718329	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718330	0.91[EUR][1000 genomes]
rs6460278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460282	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460284	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6460287	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6460290	0.90[EUR][1000 genomes]
rs6460293	0.95[EUR][1000 genomes]
rs6944374	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6951503	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6952182	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6952473	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6958294	0.96[EUR][1000 genomes]
rs6959268	0.88[EUR][1000 genomes]
rs6960446	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6962717	0.81[EUR][1000 genomes]
rs6963228	0.86[EUR][1000 genomes]
rs6964437	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6967708	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6971752	0.90[EUR][1000 genomes]
rs6974614	0.88[EUR][1000 genomes]
rs6976714	0.80[EUR][1000 genomes]
rs6977501	0.80[AFR][1000 genomes]
rs6978028	0.86[EUR][1000 genomes]
rs6979452	0.94[EUR][1000 genomes]
rs709596	0.89[EUR][1000 genomes]
rs7781880	0.82[EUR][1000 genomes]
rs7782704	0.90[EUR][1000 genomes]
rs7782806	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7783779	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs778680	0.88[EUR][1000 genomes]
rs778684	0.90[EUR][1000 genomes]
rs778686	0.90[EUR][1000 genomes]
rs7786892	0.83[EUR][1000 genomes]
rs778690	0.86[EUR][1000 genomes]
rs778697	0.86[EUR][1000 genomes]
rs778702	0.81[EUR][1000 genomes]
rs778705	0.87[EUR][1000 genomes]
rs778707	0.87[EUR][1000 genomes]
rs778711	0.87[EUR][1000 genomes]
rs778715	0.83[EUR][1000 genomes]
rs778716	0.83[EUR][1000 genomes]
rs778720	0.83[EUR][1000 genomes]
rs778724	0.90[EUR][1000 genomes]
rs778728	0.86[EUR][1000 genomes]
rs778734	0.90[EUR][1000 genomes]
rs778736	0.95[EUR][1000 genomes]
rs7787482	0.86[EUR][1000 genomes]
rs7789615	0.84[EUR][1000 genomes]
rs7796162	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7798630	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs809025	0.83[EUR][1000 genomes]
rs880166	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs949930	0.91[EUR][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	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	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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs6460279	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6460279	RP4-756H11.3	cis	lung	GTEx
rs6460279	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6460279	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460279	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6460279	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6460279	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6460279	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6460279	RNU6-96P	cis	Thyroid	GTEx
rs6460279	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6460279	RP4-756H11.3	cis	Thyroid	GTEx
rs6460279	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6460279	GS1-124K5.2	cis	Whole Blood	GTEx
rs6460279	GS1-124K5.4	cis	Stomach	GTEx
rs6460279	GS1-124K5.11	cis	Thyroid	GTEx
rs6460279	LINC00174	cis	Thyroid	GTEx
rs6460279	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6460279	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6460279	GTF2IRD1P1	cis	Thyroid	GTEx
rs6460279	RP4-756H11.3	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65660800-65669800	Weak transcription	Spleen	Spleen
2	chr7:65661600-65663200	Weak transcription	HepG2	liver
3	chr7:65661600-65669400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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