Variant report

Variant	rs298053
Chromosome Location	chr5:58915798-58915799
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	chr5:58915352..58918200-chr5:58918396..58920310,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10805516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159194	0.85[ASN][1000 genomes]
rs159196	0.89[ASN][1000 genomes]
rs159197	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs177078	0.91[ASN][1000 genomes]
rs186078	0.84[ASN][1000 genomes]
rs190936	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs294477	0.84[ASN][1000 genomes]
rs294478	0.85[ASN][1000 genomes]
rs294479	0.85[ASN][1000 genomes]
rs294481	0.85[ASN][1000 genomes]
rs294482	0.84[ASN][1000 genomes]
rs294483	0.85[ASN][1000 genomes]
rs294484	0.85[ASN][1000 genomes]
rs294485	0.83[ASN][1000 genomes]
rs294486	0.85[ASN][1000 genomes]
rs294492	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs294495	0.92[ASN][1000 genomes]
rs294496	0.92[ASN][1000 genomes]
rs294497	0.92[ASN][1000 genomes]
rs294498	0.89[ASN][1000 genomes]
rs294499	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs294500	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs294501	0.89[ASN][1000 genomes]
rs294502	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs295943	0.93[EUR][1000 genomes]
rs295944	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295948	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295950	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295951	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295953	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295954	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295956	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295957	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295958	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295960	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295963	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295964	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295965	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295966	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295968	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295969	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295970	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295972	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295973	0.99[ASN][1000 genomes]
rs295974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295975	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295978	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295979	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs295980	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs298016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298032	0.83[ASN][1000 genomes]
rs298033	0.83[ASN][1000 genomes]
rs298034	0.88[ASN][1000 genomes]
rs298036	0.91[ASN][1000 genomes]
rs298038	0.89[ASN][1000 genomes]
rs298039	0.89[ASN][1000 genomes]
rs298040	0.92[ASN][1000 genomes]
rs298041	0.93[ASN][1000 genomes]
rs298043	0.92[ASN][1000 genomes]
rs298044	0.93[ASN][1000 genomes]
rs298045	0.93[ASN][1000 genomes]
rs298046	0.92[ASN][1000 genomes]
rs298047	0.93[ASN][1000 genomes]
rs298048	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs298051	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37569	0.84[ASN][1000 genomes]
rs37570	0.85[ASN][1000 genomes]
rs37571	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58897600-58915800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:58905600-58915800	Weak transcription	HSMMtube	muscle
3	chr5:58911400-58929600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:58911800-58915800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:58911800-58916600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:58911800-58918400	Weak transcription	Hela-S3	cervix
7	chr5:58912400-58915800	Weak transcription	HSMM	muscle
8	chr5:58912600-58916000	Weak transcription	Osteobl	bone
9	chr5:58913800-58918800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:58914200-58919200	Weak transcription	Stomach Mucosa	stomach
11	chr5:58914400-58922600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:58914400-58923400	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:58914400-58923400	Weak transcription	Psoas Muscle	Psoas
14	chr5:58915200-58915800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:58915200-58915800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr5:58915200-58916000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr5:58915200-58917600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr5:58915400-58916200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr5:58915400-58916200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:58915400-58916600	Enhancers	Aorta	Aorta
21	chr5:58915400-58918200	Weak transcription	A549	lung
22	chr5:58915600-58916000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:58915600-58916200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr5:58915600-58916600	Enhancers	Primary B cells from cord blood	blood
25	chr5:58915600-58917600	Enhancers	Primary B cells from peripheral blood	blood

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