Variant report

Variant	rs56410005
Chromosome Location	chr5:112570874-112570875
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112570824..112573255-chr5:112670003..112671538,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10035647	1.00[ASN][1000 genomes]
rs10037038	1.00[ASN][1000 genomes]
rs10069434	1.00[ASN][1000 genomes]
rs10076511	1.00[ASN][1000 genomes]
rs10213689	1.00[ASN][1000 genomes]
rs10213826	1.00[ASN][1000 genomes]
rs10519339	1.00[ASN][1000 genomes]
rs10519340	1.00[ASN][1000 genomes]
rs10519342	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241199	1.00[ASN][1000 genomes]
rs11951541	1.00[ASN][1000 genomes]
rs11958840	1.00[ASN][1000 genomes]
rs13362511	1.00[ASN][1000 genomes]
rs17135464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135493	1.00[ASN][1000 genomes]
rs17135511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091802	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55967427	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104704	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57602920	1.00[ASN][1000 genomes]
rs57696719	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57948635	1.00[ASN][1000 genomes]
rs58069204	1.00[ASN][1000 genomes]
rs58237028	1.00[ASN][1000 genomes]
rs58879623	1.00[ASN][1000 genomes]
rs59101992	1.00[ASN][1000 genomes]
rs59673184	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59807191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60185446	1.00[ASN][1000 genomes]
rs60590719	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60636636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60727695	1.00[ASN][1000 genomes]
rs61643643	1.00[ASN][1000 genomes]
rs61692685	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374390	1.00[ASN][1000 genomes]
rs634261	1.00[ASN][1000 genomes]
rs6859436	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6859619	1.00[ASN][1000 genomes]
rs6874561	1.00[ASN][1000 genomes]
rs6878329	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899178	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244736	1.00[ASN][1000 genomes]
rs73244737	1.00[ASN][1000 genomes]
rs73244738	1.00[ASN][1000 genomes]
rs73244740	1.00[ASN][1000 genomes]
rs73244742	1.00[ASN][1000 genomes]
rs73244743	1.00[ASN][1000 genomes]
rs73244754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244763	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244773	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244797	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73246617	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702837	1.00[ASN][1000 genomes]
rs7708947	1.00[ASN][1000 genomes]
rs7710138	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7723474	1.00[ASN][1000 genomes]
rs9326885	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112548400-112581800	Weak transcription	Fetal Kidney	kidney
2	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:112559000-112571200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:112561600-112575000	Weak transcription	Right Ventricle	heart
5	chr5:112565400-112572000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:112566200-112572400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:112566400-112571000	Enhancers	Adipose Nuclei	Adipose
8	chr5:112566400-112571200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr5:112566400-112572400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:112566400-112574000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:112567200-112571000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:112567200-112572400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:112567200-112572400	Enhancers	NHEK	skin
14	chr5:112567400-112571200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:112567400-112572800	Enhancers	Stomach Mucosa	stomach
16	chr5:112567400-112573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:112568000-112571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:112568400-112572400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:112568600-112575000	Weak transcription	Left Ventricle	heart
20	chr5:112568800-112572200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:112568800-112572600	Weak transcription	Psoas Muscle	Psoas
22	chr5:112568800-112573000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:112568800-112575200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr5:112569000-112575400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr5:112569000-112577800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:112569200-112571200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:112569400-112571400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:112569400-112573400	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:112569600-112572400	Weak transcription	Fetal Brain Male	brain
30	chr5:112569600-112574000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:112569600-112575400	Weak transcription	Fetal Brain Female	brain
32	chr5:112569800-112572200	Weak transcription	Fetal Lung	lung
33	chr5:112569800-112573200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr5:112570000-112572200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr5:112570000-112574000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:112570200-112572600	Enhancers	HMEC	breast
37	chr5:112570200-112573600	Weak transcription	Fetal Stomach	stomach
38	chr5:112570200-112574000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:112570200-112576200	Enhancers	Fetal Heart	heart
40	chr5:112570400-112571400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:112570400-112571800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:112570400-112572400	Enhancers	Liver	Liver
43	chr5:112570600-112572800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr5:112570800-112571600	Weak transcription	Esophagus	oesophagus
45	chr5:112570800-112572000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:112570800-112572600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:112570800-112573200	Weak transcription	Right Atrium	heart
48	chr5:112570800-112573600	Weak transcription	Ovary	ovary
49	chr5:112570800-112580600	Weak transcription	Fetal Muscle Leg	muscle

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