Variant report

Variant	rs12109713
Chromosome Location	chr5:126416187-126416188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126416173..126417766-chr5:126424953..126426856,2	MCF-7	breast:
2	chr5:126408546..126411993-chr5:126414423..126416954,3	MCF-7	breast:
3	chr5:126414653..126417041-chr5:126422824..126425859,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164241	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11949784	0.94[EUR][1000 genomes]
rs11950032	0.83[EUR][1000 genomes]
rs11952890	0.94[EUR][1000 genomes]
rs11959383	0.94[EUR][1000 genomes]
rs58134448	0.89[EUR][1000 genomes]
rs58159475	0.95[EUR][1000 genomes]
rs61146816	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6860157	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339263	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339286	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73783512	1.00[EUR][1000 genomes]
rs73783538	0.94[EUR][1000 genomes]
rs73783539	0.94[EUR][1000 genomes]
rs73783540	0.94[EUR][1000 genomes]
rs73783541	0.94[EUR][1000 genomes]
rs73783556	0.94[EUR][1000 genomes]
rs73783557	0.94[EUR][1000 genomes]
rs73783560	0.94[EUR][1000 genomes]
rs73783575	0.94[EUR][1000 genomes]
rs73783579	0.94[EUR][1000 genomes]
rs73783580	0.94[EUR][1000 genomes]
rs73786204	0.83[EUR][1000 genomes]
rs73787407	0.94[EUR][1000 genomes]
rs73787408	0.94[EUR][1000 genomes]
rs9918170	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1816248	chr5:126399039-126486539	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126412600-126427400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:126413200-126417000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:126413600-126421800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:126413600-126424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:126413600-126428000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:126414000-126416200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:126415000-126417000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:126415200-126416800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:126415200-126416800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:126415200-126416800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr5:126415200-126416800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:126415400-126416800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr5:126415400-126416800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:126415400-126416800	Enhancers	HMEC	breast
15	chr5:126415400-126417200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:126415600-126416200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:126415600-126416200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:126415600-126416200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:126415600-126416200	Enhancers	Placenta	Placenta
20	chr5:126415600-126416200	Enhancers	NHEK	skin
21	chr5:126415600-126416400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:126415600-126416400	Enhancers	Fetal Intestine Small	intestine
23	chr5:126415600-126416400	Enhancers	K562	blood
24	chr5:126415600-126416600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:126415600-126417000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr5:126415600-126417000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:126415600-126417000	Enhancers	Fetal Intestine Large	intestine
28	chr5:126415800-126416400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:126415800-126416600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr5:126415800-126416800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr5:126415800-126417000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:126416000-126416200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:126416000-126416200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:126416000-126416400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:126416000-126416400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:126416000-126416800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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