Variant report

Variant	rs11773456
Chromosome Location	chr7:64401406-64401407
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	chr7:64365012..64367238-chr7:64400877..64402549,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11773228	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13223142	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13225933	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13236444	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13236784	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1830007	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1966140	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017252	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34238742	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35058955	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35065007	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3813700	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829003	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4644117	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4717222	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718156	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718169	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4718170	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56063644	0.89[EUR][1000 genomes]
rs62455121	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62458435	0.86[EUR][1000 genomes]
rs6460209	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6953002	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6957266	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7776640	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782713	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7786519	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7796024	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7796284	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7797115	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7798063	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7798465	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7805817	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9638209	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv888282	chr7:64299645-64511564	Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	esv3506582	chr7:64323055-64563984	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	esv3506583	chr7:64323055-64563984	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1019180	chr7:64329889-64512842	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv888283	chr7:64343985-64511564	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	esv2752165	chr7:64345822-65208605	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:44)

SNP	Gene	Cis/trans	Tissue	Source
rs11773456	SEPHS1P1	cis	Thyroid	GTEx
rs11773456	RP11-460N20.5	cis	lung	GTEx
rs11773456	CCT6P3	cis	Skin Sun Exposed Lower leg	GTEx
rs11773456	RP11-460N20.4	cis	Adipose Subcutaneous	GTEx
rs11773456	RP11-797H7.5	cis	Artery Tibial	GTEx
rs11773456	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs11773456	RP11-797H7.3	cis	lung	GTEx
rs11773456	RP11-460N20.5	cis	Whole Blood	GTEx
rs11773456	CCT6P3	cis	lung	GTEx
rs11773456	RP11-797H7.5	cis	lung	GTEx
rs11773456	SEPHS1P1	cis	Muscle Skeletal	GTEx
rs11773456	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs11773456	RP11-797H7.5	cis	Adipose Subcutaneous	GTEx
rs11773456	RP11-797H7.5	cis	Esophagus Muscularis	GTEx
rs11773456	RP11-797H7.3	cis	Artery Aorta	GTEx
rs11773456	SEPHS1P1	cis	Nerve Tibial	GTEx
rs11773456	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs11773456	RP11-667F9.1	cis	Nerve Tibial	GTEx
rs11773456	CCT6P3	cis	Artery Tibial	GTEx
rs11773456	RP11-797H7.3	cis	Esophagus Muscularis	GTEx
rs11773456	CCT6P3	cis	Adipose Subcutaneous	GTEx
rs11773456	RP11-460N20.5	cis	Nerve Tibial	GTEx
rs11773456	RP11-797H7.5	cis	Skin Sun Exposed Lower leg	GTEx
rs11773456	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs11773456	RP11-797H7.3	cis	Whole Blood	GTEx
rs11773456	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11773456	CCT6P3	cis	Esophagus Mucosa	GTEx
rs11773456	RP11-797H7.3	cis	Artery Tibial	GTEx
rs11773456	RP11-797H7.3	cis	Thyroid	GTEx
rs11773456	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs11773456	INTS4L1	cis	Nerve Tibial	GTEx
rs11773456	RP11-797H7.5	cis	Thyroid	GTEx
rs11773456	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs11773456	CCT6P3	cis	Nerve Tibial	GTEx
rs11773456	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs11773456	SEPHS1P1	cis	Artery Tibial	GTEx
rs11773456	SEPHS1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs11773456	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs11773456	ZNF273	cis	lung	GTEx
rs11773456	RP11-460N20.5	cis	Artery Tibial	GTEx
rs11773456	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs11773456	RP11-460N20.5	cis	Thyroid	GTEx
rs11773456	RP11-667F9.1	cis	Adipose Subcutaneous	GTEx
rs11773456	ZNF273	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64387800-64402200	Weak transcription	Left Ventricle	heart
2	chr7:64389200-64402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:64390600-64403000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:64390800-64406400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:64397200-64407000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:64397400-64403000	Weak transcription	Spleen	Spleen
7	chr7:64399800-64402600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:64400600-64407600	Weak transcription	Right Atrium	heart

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