Variant report

Variant	rs28419463
Chromosome Location	chr4:53700770-53700771
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	chr4:53697493..53701667-chr4:53702709..53704806,3	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10001855	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10008073	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10014464	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043975	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11930907	0.83[ASN][1000 genomes]
rs11934293	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11941562	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1483685	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1483686	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1483687	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17082081	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17082143	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17082147	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1963003	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003198	0.83[ASN][1000 genomes]
rs2017237	0.84[ASN][1000 genomes]
rs2046364	0.84[ASN][1000 genomes]
rs2062253	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2200226	0.86[ASN][1000 genomes]
rs2279334	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306601	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2411259	0.81[EUR][1000 genomes]
rs2411281	0.83[ASN][1000 genomes]
rs28454903	0.81[EUR][1000 genomes]
rs28489424	0.81[EUR][1000 genomes]
rs28526700	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28704139	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28733375	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28735908	0.81[EUR][1000 genomes]
rs28811693	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898681	0.83[ASN][1000 genomes]
rs301135	0.80[AMR][1000 genomes]
rs301136	0.80[AMR][1000 genomes]
rs4242020	0.81[EUR][1000 genomes]
rs4309903	0.81[EUR][1000 genomes]
rs4864673	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4864679	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864681	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864682	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864683	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864688	0.84[ASN][1000 genomes]
rs4864690	0.83[ASN][1000 genomes]
rs4864691	0.83[ASN][1000 genomes]
rs4865422	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4990628	0.81[EUR][1000 genomes]
rs5012592	0.81[EUR][1000 genomes]
rs59649036	0.84[ASN][1000 genomes]
rs61268502	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62336785	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62336788	0.97[EUR][1000 genomes]
rs62336791	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336792	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336794	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62336795	0.85[ASN][1000 genomes]
rs62336823	0.80[ASN][1000 genomes]
rs62338801	0.81[EUR][1000 genomes]
rs62338805	0.81[EUR][1000 genomes]
rs6833096	0.83[ASN][1000 genomes]
rs6839084	0.83[ASN][1000 genomes]
rs6852148	0.84[ASN][1000 genomes]
rs73143042	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs900607	0.86[ASN][1000 genomes]
rs922932	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs922933	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9993034	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53691800-53704000	Weak transcription	Right Atrium	heart
2	chr4:53692200-53704000	Weak transcription	Right Ventricle	heart
3	chr4:53698600-53701000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr4:53698800-53710600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr4:53699200-53701800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:53699200-53701800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:53699800-53701000	Enhancers	HMEC	breast
8	chr4:53699800-53701400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:53699800-53701600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr4:53699800-53701600	Enhancers	NHEK	skin
11	chr4:53700000-53700800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:53700000-53701000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:53700000-53701000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:53700000-53702600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr4:53700000-53703000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:53700000-53704800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr4:53700200-53700800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr4:53700200-53700800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:53700200-53700800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr4:53700200-53700800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr4:53700200-53701000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:53700200-53701000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:53700200-53701000	Enhancers	Esophagus	oesophagus
24	chr4:53700200-53701000	Enhancers	Left Ventricle	heart
25	chr4:53700200-53701000	Enhancers	Psoas Muscle	Psoas
26	chr4:53700200-53703000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:53700200-53710800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr4:53700400-53700800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:53700400-53700800	Enhancers	Fetal Heart	heart
30	chr4:53700400-53700800	Enhancers	Osteobl	bone
31	chr4:53700400-53701000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:53700400-53701000	Enhancers	Stomach Mucosa	stomach
33	chr4:53700400-53701400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:53700400-53702200	Weak transcription	NHDF-Ad	bronchial
35	chr4:53700400-53702400	Weak transcription	Ovary	ovary
36	chr4:53700400-53709600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr4:53700600-53700800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr4:53700600-53701000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:53700600-53703800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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