Variant report

Variant	rs11952524
Chromosome Location	chr5:127878675-127878676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127873521..127875105-chr5:127878457..127880160,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138829	Chromatin interaction
ENSG00000113396	Chromatin interaction

Extended variants
information (count: 189 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:185)

rs_ID	r²[population]
rs10520003	1.00[ASN][1000 genomes]
rs11241962	1.00[ASN][1000 genomes]
rs11241964	1.00[ASN][1000 genomes]
rs11241965	1.00[ASN][1000 genomes]
rs11948376	1.00[ASN][1000 genomes]
rs11948920	1.00[ASN][1000 genomes]
rs11949017	1.00[ASN][1000 genomes]
rs11949649	1.00[ASN][1000 genomes]
rs11949660	1.00[ASN][1000 genomes]
rs11949692	1.00[ASN][1000 genomes]
rs11950568	1.00[ASN][1000 genomes]
rs11950625	1.00[ASN][1000 genomes]
rs11951267	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11952247	1.00[ASN][1000 genomes]
rs11952334	1.00[ASN][1000 genomes]
rs11952602	1.00[ASN][1000 genomes]
rs11953201	1.00[ASN][1000 genomes]
rs11954034	1.00[ASN][1000 genomes]
rs11954070	1.00[ASN][1000 genomes]
rs11955937	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11956467	1.00[ASN][1000 genomes]
rs11956495	1.00[ASN][1000 genomes]
rs11957280	1.00[ASN][1000 genomes]
rs11957487	1.00[ASN][1000 genomes]
rs11958508	1.00[ASN][1000 genomes]
rs11958996	1.00[ASN][1000 genomes]
rs11959560	1.00[ASN][1000 genomes]
rs13153812	1.00[ASN][1000 genomes]
rs13160701	1.00[ASN][1000 genomes]
rs13168271	1.00[ASN][1000 genomes]
rs1435512	1.00[ASN][1000 genomes]
rs17164083	1.00[ASN][1000 genomes]
rs17164086	1.00[ASN][1000 genomes]
rs17615636	1.00[ASN][1000 genomes]
rs17677244	1.00[ASN][1000 genomes]
rs34012094	1.00[ASN][1000 genomes]
rs34139509	1.00[ASN][1000 genomes]
rs34615740	1.00[ASN][1000 genomes]
rs34665677	1.00[ASN][1000 genomes]
rs34881645	1.00[ASN][1000 genomes]
rs35043622	1.00[ASN][1000 genomes]
rs36003105	1.00[ASN][1000 genomes]
rs36052309	1.00[ASN][1000 genomes]
rs36071106	1.00[ASN][1000 genomes]
rs36125852	1.00[ASN][1000 genomes]
rs3924302	1.00[ASN][1000 genomes]
rs4133248	1.00[ASN][1000 genomes]
rs4318822	1.00[ASN][1000 genomes]
rs4339399	1.00[ASN][1000 genomes]
rs4345355	1.00[ASN][1000 genomes]
rs4365880	1.00[ASN][1000 genomes]
rs4380709	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4386769	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4400171	0.87[AFR][1000 genomes]
rs4410683	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4425555	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4425556	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4455613	1.00[ASN][1000 genomes]
rs4493715	1.00[ASN][1000 genomes]
rs4496752	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4557470	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4577751	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4580821	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4582335	1.00[ASN][1000 genomes]
rs4620068	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4628037	1.00[ASN][1000 genomes]
rs4628038	1.00[ASN][1000 genomes]
rs4836374	1.00[ASN][1000 genomes]
rs55657505	1.00[ASN][1000 genomes]
rs55683423	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55715053	1.00[ASN][1000 genomes]
rs55770077	1.00[ASN][1000 genomes]
rs55791343	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55839668	1.00[ASN][1000 genomes]
rs55944506	1.00[ASN][1000 genomes]
rs56018106	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56072924	1.00[ASN][1000 genomes]
rs56173634	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56232757	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56766733	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57454105	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58143160	1.00[ASN][1000 genomes]
rs58295967	1.00[ASN][1000 genomes]
rs58955919	1.00[ASN][1000 genomes]
rs59143127	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59567527	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60324229	1.00[ASN][1000 genomes]
rs60574263	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61358597	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61375240	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62390696	1.00[ASN][1000 genomes]
rs62390705	1.00[ASN][1000 genomes]
rs62390715	1.00[ASN][1000 genomes]
rs62390716	1.00[ASN][1000 genomes]
rs62390718	1.00[ASN][1000 genomes]
rs62390719	1.00[ASN][1000 genomes]
rs62390724	1.00[ASN][1000 genomes]
rs62390725	1.00[ASN][1000 genomes]
rs62390726	1.00[ASN][1000 genomes]
rs6595840	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs66899065	1.00[ASN][1000 genomes]
rs67539441	1.00[ASN][1000 genomes]
rs67941180	1.00[ASN][1000 genomes]
rs6863062	1.00[ASN][1000 genomes]
rs6863262	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6863380	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6863460	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6864449	1.00[ASN][1000 genomes]
rs6865828	1.00[ASN][1000 genomes]
rs6870737	1.00[ASN][1000 genomes]
rs6870746	1.00[ASN][1000 genomes]
rs6871698	1.00[ASN][1000 genomes]
rs6875600	1.00[ASN][1000 genomes]
rs6876597	1.00[ASN][1000 genomes]
rs6876609	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6877748	1.00[ASN][1000 genomes]
rs6877872	1.00[ASN][1000 genomes]
rs6877956	1.00[ASN][1000 genomes]
rs6878062	1.00[ASN][1000 genomes]
rs6878172	1.00[ASN][1000 genomes]
rs6880762	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6885752	1.00[ASN][1000 genomes]
rs6886451	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6891153	1.00[ASN][1000 genomes]
rs6891166	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6892406	1.00[ASN][1000 genomes]
rs6897170	1.00[ASN][1000 genomes]
rs6898190	1.00[ASN][1000 genomes]
rs73334912	1.00[ASN][1000 genomes]
rs73346354	1.00[ASN][1000 genomes]
rs73348066	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348070	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348077	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348078	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348080	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348085	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348087	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348099	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348102	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348278	1.00[ASN][1000 genomes]
rs73348280	1.00[ASN][1000 genomes]
rs73348283	1.00[ASN][1000 genomes]
rs73348287	1.00[ASN][1000 genomes]
rs73348295	1.00[ASN][1000 genomes]
rs73348296	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73348299	1.00[ASN][1000 genomes]
rs73350104	0.87[AFR][1000 genomes]
rs73350106	1.00[ASN][1000 genomes]
rs73350109	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73350115	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73350129	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73350134	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73350195	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73352205	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73352207	1.00[ASN][1000 genomes]
rs73352225	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7443826	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7443867	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7446246	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7446266	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7446359	1.00[ASN][1000 genomes]
rs7447218	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs764369	1.00[ASN][1000 genomes]
rs7700287	0.87[AFR][1000 genomes]
rs7704921	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7709202	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7709476	1.00[ASN][1000 genomes]
rs7709634	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7712769	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714023	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7714465	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7714623	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7720190	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7724233	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7724383	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7725452	1.00[ASN][1000 genomes]
rs7725949	1.00[ASN][1000 genomes]
rs7727413	1.00[ASN][1000 genomes]
rs7728409	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7730875	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7732171	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7734405	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7734534	1.00[ASN][1000 genomes]
rs7735831	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs892864	1.00[ASN][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	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11952524	FBN2	cis	Thyroid	GTEx
rs11952524	FBN2	cis	Adipose Subcutaneous	GTEx
rs11952524	FBN2	cis	Artery Aorta	GTEx
rs11952524	FBN2	cis	Whole Blood	GTEx
rs11952524	FBN2	cis	Nerve Tibial	GTEx
rs11952524	FBN2	cis	Artery Tibial	GTEx
rs11952524	FBN2	cis	lung	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127875200-127882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:127875400-127882400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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