Variant report

Variant	rs28494592
Chromosome Location	chr5:112601406-112601407
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	chr5:112597661..112600348-chr5:112601306..112603277,2	MCF-7	breast:
2	chr5:112543815..112546269-chr5:112600639..112603401,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10038017	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040533	0.94[EUR][1000 genomes]
rs10040770	1.00[EUR][1000 genomes]
rs10044201	0.94[EUR][1000 genomes]
rs10051109	0.94[EUR][1000 genomes]
rs10058535	0.94[EUR][1000 genomes]
rs10059129	0.94[EUR][1000 genomes]
rs10070990	0.94[EUR][1000 genomes]
rs10074346	0.94[EUR][1000 genomes]
rs10075447	0.94[EUR][1000 genomes]
rs10478121	0.94[EUR][1000 genomes]
rs10519344	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11953478	0.94[EUR][1000 genomes]
rs11954016	0.94[EUR][1000 genomes]
rs11954410	0.94[EUR][1000 genomes]
rs11958734	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12108831	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13356396	0.81[EUR][1000 genomes]
rs13361059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13361060	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13362158	0.94[EUR][1000 genomes]
rs17135493	0.85[EUR][1000 genomes]
rs1882620	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2068922	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55794576	0.94[EUR][1000 genomes]
rs56875463	0.94[EUR][1000 genomes]
rs6874561	0.85[EUR][1000 genomes]
rs73779001	1.00[EUR][1000 genomes]
rs73779022	0.94[EUR][1000 genomes]
rs73781513	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73781514	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7700940	0.89[EUR][1000 genomes]
rs7719166	0.94[EUR][1000 genomes]
rs9285877	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9326881	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9326882	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9326883	0.93[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
3	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:112589200-112610600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:112589400-112602200	Weak transcription	Esophagus	oesophagus
6	chr5:112591600-112602000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:112594400-112602200	Weak transcription	Left Ventricle	heart
8	chr5:112594400-112602200	Weak transcription	Right Ventricle	heart
9	chr5:112595200-112601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:112595600-112602200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:112598800-112603800	Enhancers	Liver	Liver
12	chr5:112599400-112603000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:112599800-112602000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:112599800-112602200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:112599800-112604800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:112600000-112601600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:112600000-112602000	Weak transcription	Adipose Nuclei	Adipose
18	chr5:112600200-112602000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:112600200-112604800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:112600200-112605000	Weak transcription	NH-A	brain
21	chr5:112600200-112618000	Weak transcription	Fetal Kidney	kidney
22	chr5:112600400-112605200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:112600600-112602400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr5:112600800-112602800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr5:112600800-112602800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr5:112600800-112605000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:112600800-112607200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr5:112600800-112607600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr5:112600800-112608000	Enhancers	Ovary	ovary
30	chr5:112600800-112610600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:112600800-112610800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr5:112601000-112602600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:112601000-112603400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr5:112601000-112604000	Enhancers	Fetal Heart	heart
35	chr5:112601000-112606200	Enhancers	Right Atrium	heart
36	chr5:112601000-112612400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr5:112601200-112602400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:112601200-112602400	Enhancers	HMEC	breast
39	chr5:112601200-112603800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr5:112601200-112605000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:112601200-112605800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:112601400-112601600	Enhancers	Fetal Lung	lung
43	chr5:112601400-112602200	Enhancers	Brain Hippocampus Middle	brain
44	chr5:112601400-112602200	Weak transcription	Placenta	Placenta
45	chr5:112601400-112602200	Enhancers	NHEK	skin
46	chr5:112601400-112611200	Enhancers	Pancreatic Islets	Pancreatic Islet

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