Variant report

Variant	rs11772884
Chromosome Location	chr7:66066637-66066638
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	chr7:66065925..66067738-chr7:66091765..66093864,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10107	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10265311	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10271548	0.84[AMR][1000 genomes]
rs10274883	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10278014	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950043	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12333370	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12673450	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12698522	0.86[AMR][1000 genomes]
rs12698526	0.86[AMR][1000 genomes]
rs13226170	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13232191	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13240501	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13242290	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13308803	0.81[EUR][1000 genomes]
rs13536	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17747530	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1860469	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1860472	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1968126	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2013908	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2024192	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109295	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2109297	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2420610	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2420611	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2420821	0.81[AMR][1000 genomes]
rs2659890	0.81[EUR][1000 genomes]
rs2659891	0.81[EUR][1000 genomes]
rs2659892	0.81[EUR][1000 genomes]
rs2659893	0.81[EUR][1000 genomes]
rs2659898	0.81[EUR][1000 genomes]
rs2659901	0.81[EUR][1000 genomes]
rs2659907	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2659908	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2707824	0.81[EUR][1000 genomes]
rs2707847	0.81[EUR][1000 genomes]
rs28480509	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28617601	0.86[AMR][1000 genomes]
rs28714531	0.87[AMR][1000 genomes]
rs28731376	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35378740	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3846973	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3926380	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4717315	0.81[EUR][1000 genomes]
rs4718377	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4718383	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61348003	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6460303	0.87[AMR][1000 genomes]
rs66981195	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6951302	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6951946	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6955837	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6958200	0.81[AMR][1000 genomes]
rs6971059	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6973249	0.88[AMR][1000 genomes]
rs6978178	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs721717	0.80[AMR][1000 genomes]
rs7384021	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7385102	0.94[AMR][1000 genomes]
rs7782587	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7793723	0.82[AMR][1000 genomes]
rs7808013	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs801194	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs801195	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs801202	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs801203	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs801204	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs801206	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs801208	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs801209	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs801215	0.84[AMR][1000 genomes]
rs881285	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9791712	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9791713	0.86[AMR][1000 genomes];0.86[EUR][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	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
2	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
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11772884	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs11772884	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11772884	GTF2IRD1P1	cis	Thyroid	GTEx
rs11772884	RP4-756H11.3	cis	lung	GTEx
rs11772884	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs11772884	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs11772884	GS1-124K5.4	cis	Artery Aorta	GTEx
rs11772884	GS1-124K5.4	cis	Whole Blood	GTEx
rs11772884	LINC00174	cis	Thyroid	GTEx
rs11772884	RNU6-96P	cis	Thyroid	GTEx
rs11772884	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs11772884	RP4-756H11.3	cis	Thyroid	GTEx
rs11772884	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs11772884	RP4-756H11.3	cis	Artery Tibial	GTEx
rs11772884	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs11772884	GS1-124K5.11	cis	Thyroid	GTEx
rs11772884	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs11772884	ASL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66057600-66067600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66058000-66067600	Weak transcription	Lung	lung
3	chr7:66058200-66067000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:66058200-66068800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:66064600-66067000	Weak transcription	HepG2	liver

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