Variant report

Variant	rs2389872
Chromosome Location	chr4:120554040-120554041
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	chr4:120552728..120554364-chr4:120974086..120975727,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10013852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10021469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10434030	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10434031	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10434032	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10434033	0.82[ASN][1000 genomes]
rs10518332	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10518333	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12331661	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17007472	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051276	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051278	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17357002	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17359764	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359910	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17360333	0.90[EUR][1000 genomes]
rs1962195	0.82[ASN][1000 genomes]
rs2389871	0.92[AFR][1000 genomes]
rs2389876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389877	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389878	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389883	0.82[ASN][1000 genomes]
rs2389884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389891	0.82[ASN][1000 genomes]
rs2389892	0.82[ASN][1000 genomes]
rs2953290	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953294	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3109370	0.83[AMR][1000 genomes]
rs4102980	0.82[EUR][1000 genomes]
rs4146266	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833621	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58613543	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58735454	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59225699	0.82[ASN][1000 genomes]
rs6534145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6534148	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6831062	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6854072	0.88[AFR][1000 genomes]
rs72922580	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72922588	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72922598	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72924305	0.82[ASN][1000 genomes]
rs72924312	0.82[ASN][1000 genomes]
rs7671191	0.82[ASN][1000 genomes]
rs7684853	0.82[ASN][1000 genomes]
rs8180145	0.85[ASN][1000 genomes]
rs8180147	0.85[ASN][1000 genomes]
rs9991735	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3466099	chr4:120552743-120556240	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3466100	chr4:120552768-120556201	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3466098	chr4:120552770-120556212	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3466102	chr4:120552788-120556162	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3466101	chr4:120552835-120556137	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv17708	chr4:120552839-120556129	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3466103	chr4:120552849-120556136	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120550600-120554400	Weak transcription	Pancreas	Pancrea
2	chr4:120552200-120554200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:120552400-120558600	Weak transcription	Fetal Stomach	stomach
4	chr4:120553600-120554200	Enhancers	Osteobl	bone
5	chr4:120554000-120559400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:120554000-120559400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:120554000-120559400	Weak transcription	NHLF	lung

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