Variant report

Variant	rs298043
Chromosome Location	chr5:58924870-58924871
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	chr5:58919593..58921213-chr5:58924380..58926616,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10805516	0.92[ASN][1000 genomes]
rs159194	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs159196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs159197	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs177077	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs177078	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs190936	0.92[ASN][1000 genomes]
rs294478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs294479	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs294481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs294482	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs294483	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs294484	1.00[CHB][hapmap]
rs294485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs294486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs294492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs294494	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294495	0.84[ASN][1000 genomes]
rs294496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs294497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs294498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs294499	0.83[ASN][1000 genomes]
rs294500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs294501	0.82[ASN][1000 genomes]
rs294502	0.80[ASN][1000 genomes]
rs295943	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs295946	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295948	0.83[ASN][1000 genomes]
rs295950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295951	0.88[ASN][1000 genomes]
rs295952	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs295953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295955	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs295956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295957	0.88[ASN][1000 genomes]
rs295958	0.89[ASN][1000 genomes]
rs295960	0.89[ASN][1000 genomes]
rs295962	0.92[ASN][1000 genomes]
rs295963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs295964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs295965	0.92[ASN][1000 genomes]
rs295966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs295967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs295968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs295969	0.92[ASN][1000 genomes]
rs295970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs295971	0.92[ASN][1000 genomes]
rs295972	0.92[ASN][1000 genomes]
rs295973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs295974	0.92[ASN][1000 genomes]
rs295975	0.92[ASN][1000 genomes]
rs295978	0.85[ASN][1000 genomes]
rs295979	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs298014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs298016	0.92[ASN][1000 genomes]
rs298017	0.92[ASN][1000 genomes]
rs298025	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs298027	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs298028	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs298029	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs298030	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs298032	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs298033	0.91[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298034	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298036	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298037	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs298038	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298039	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298040	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298041	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs298044	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs298045	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs298046	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298047	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs298048	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298051	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs298052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs298053	0.92[ASN][1000 genomes]
rs37569	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs37571	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv598256	chr5:58893286-58939840	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv598257	chr5:58905769-58946639	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58911400-58929600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:58919400-58928200	Weak transcription	Gastric	stomach
3	chr5:58920400-58925000	Weak transcription	A549	lung
4	chr5:58921200-58926600	Weak transcription	Hela-S3	cervix
5	chr5:58921400-58926000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:58923600-58957200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:58923800-58945000	Weak transcription	Aorta	Aorta
8	chr5:58924400-58925200	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr5:58924600-58926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:58924800-58925200	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:58924800-58925600	Enhancers	Psoas Muscle	Psoas

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