Variant report

Variant	rs9784504
Chromosome Location	chr4:28623187-28623188
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	chr4:28619270..28620926-chr4:28622787..28624765,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10021733	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027922	0.91[ASN][1000 genomes]
rs10805278	1.00[ASN][1000 genomes]
rs12501893	0.91[ASN][1000 genomes]
rs12505899	0.91[ASN][1000 genomes]
rs12641531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648642	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1303817	0.82[ASN][1000 genomes]
rs1303818	0.82[ASN][1000 genomes]
rs1303819	0.82[ASN][1000 genomes]
rs13123915	0.82[ASN][1000 genomes]
rs13125329	0.82[ASN][1000 genomes]
rs13132764	0.82[ASN][1000 genomes]
rs13147296	0.82[ASN][1000 genomes]
rs1389178	1.00[ASN][1000 genomes]
rs1493150	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514126	0.91[ASN][1000 genomes]
rs1514128	0.91[ASN][1000 genomes]
rs1514129	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1565703	1.00[ASN][1000 genomes]
rs167104	0.91[ASN][1000 genomes]
rs182378	0.82[ASN][1000 genomes]
rs2047031	1.00[ASN][1000 genomes]
rs2221775	0.82[ASN][1000 genomes]
rs2248575	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458606	0.91[ASN][1000 genomes]
rs2458607	0.91[ASN][1000 genomes]
rs2458608	0.91[ASN][1000 genomes]
rs2458613	0.91[ASN][1000 genomes]
rs2458614	0.91[ASN][1000 genomes]
rs2458616	0.91[ASN][1000 genomes]
rs2458617	0.91[ASN][1000 genomes]
rs2458618	0.91[ASN][1000 genomes]
rs2458619	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458621	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2458624	0.91[ASN][1000 genomes]
rs2458626	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458627	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458628	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458629	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2458630	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471685	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471687	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471688	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2471689	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471690	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471691	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471692	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471703	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471705	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471707	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471709	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471710	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471711	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471715	0.91[ASN][1000 genomes]
rs2471717	0.91[ASN][1000 genomes]
rs2471718	0.91[ASN][1000 genomes]
rs2471719	0.91[ASN][1000 genomes]
rs2471720	0.91[ASN][1000 genomes]
rs2471721	0.91[ASN][1000 genomes]
rs2666117	0.82[ASN][1000 genomes]
rs28406281	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28645352	0.82[ASN][1000 genomes]
rs292014	0.82[ASN][1000 genomes]
rs292034	0.82[ASN][1000 genomes]
rs292049	0.82[ASN][1000 genomes]
rs292055	0.82[ASN][1000 genomes]
rs292057	0.82[ASN][1000 genomes]
rs292060	0.82[ASN][1000 genomes]
rs292072	0.82[ASN][1000 genomes]
rs292076	0.82[ASN][1000 genomes]
rs292078	0.82[ASN][1000 genomes]
rs292079	0.82[ASN][1000 genomes]
rs292082	0.82[ASN][1000 genomes]
rs292084	0.82[ASN][1000 genomes]
rs292085	0.82[ASN][1000 genomes]
rs2943155	0.91[ASN][1000 genomes]
rs2943156	0.91[ASN][1000 genomes]
rs2943157	0.91[ASN][1000 genomes]
rs2943158	0.91[ASN][1000 genomes]
rs2943160	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960592	0.91[ASN][1000 genomes]
rs2995111	0.91[ASN][1000 genomes]
rs4234996	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234997	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4280716	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4367162	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377578	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382025	1.00[ASN][1000 genomes]
rs4472125	1.00[ASN][1000 genomes]
rs4605640	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4692334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4692335	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4692340	1.00[ASN][1000 genomes]
rs4692341	1.00[ASN][1000 genomes]
rs4692343	1.00[ASN][1000 genomes]
rs542264	0.82[ASN][1000 genomes]
rs55684803	0.82[ASN][1000 genomes]
rs557255	0.91[ASN][1000 genomes]
rs567993	0.82[ASN][1000 genomes]
rs569100	0.82[ASN][1000 genomes]
rs611376	0.82[ASN][1000 genomes]
rs673272	0.82[ASN][1000 genomes]
rs687535	0.82[ASN][1000 genomes]
rs702	1.00[ASN][1000 genomes]
rs7655105	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7672198	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7695696	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790669	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010133	chr4:28273244-28642942	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1014938	chr4:28277683-28642942	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757926	chr4:28543958-28839437	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759239	chr4:28543958-28839437	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv878781	chr4:28568780-28680520	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv829894	chr4:28587323-28740840	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv1848641	chr4:28588964-28760835	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv461313	chr4:28592154-28661526	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv593893	chr4:28592154-28661526	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9784504	SEPSECS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28588200-28623400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:28622800-28623800	Enhancers	Muscle Satellite Cultured Cells	--
3	chr4:28623000-28623600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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