Variant report

Variant	rs4864680
Chromosome Location	chr4:53708421-53708422
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53707871..53710353-chr4:53715522..53717667,2	MCF-7	breast:
2	chr4:53705671..53708824-chr4:53710798..53715308,4	MCF-7	breast:
3	chr4:53707171..53710992-chr4:53726798..53730468,4	MCF-7	breast:
4	chr4:53576916..53581689-chr4:53705110..53710230,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212588	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000128045	Chromatin interaction
ENSG00000226950	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10003908	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10016904	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10023440	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10026162	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10032190	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11940896	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11941841	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11947787	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017237	0.82[AMR][1000 genomes]
rs4864676	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4864678	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4864685	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59649036	0.82[AMR][1000 genomes]
rs62336790	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62336795	0.80[AMR][1000 genomes]
rs62338810	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6554056	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6844680	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs730246	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs730247	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs731073	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7663943	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7692692	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8287	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs881743	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs936690	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs962416	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9995861	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[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:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53698800-53710600	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr4:53700200-53710800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:53700400-53709600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:53702400-53709200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:53702400-53709800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:53703800-53709000	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr4:53704000-53709200	Enhancers	Psoas Muscle	Psoas
8	chr4:53704000-53709200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr4:53704000-53709400	Enhancers	Fetal Heart	heart
10	chr4:53704000-53709600	Enhancers	Left Ventricle	heart
11	chr4:53704000-53710000	Enhancers	Fetal Muscle Leg	muscle
12	chr4:53704200-53709800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:53704600-53709400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:53705000-53709400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:53705800-53709400	Enhancers	Ovary	ovary
16	chr4:53706000-53710000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr4:53706600-53709600	Enhancers	Fetal Lung	lung
18	chr4:53706800-53709000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr4:53706800-53709400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr4:53706800-53709400	Enhancers	Stomach Mucosa	stomach
21	chr4:53706800-53710400	Enhancers	Placenta	Placenta
22	chr4:53707200-53709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:53707600-53709000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:53707600-53709200	Enhancers	Colon Smooth Muscle	Colon
25	chr4:53707600-53709400	Enhancers	Fetal Stomach	stomach
26	chr4:53707800-53708600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:53707800-53708600	Enhancers	Aorta	Aorta
28	chr4:53707800-53708600	Enhancers	Pancreas	Pancrea
29	chr4:53707800-53708600	Enhancers	Rectal Smooth Muscle	rectum
30	chr4:53707800-53708600	Enhancers	NHDF-Ad	bronchial
31	chr4:53707800-53708800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:53707800-53708800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr4:53707800-53709200	Enhancers	Gastric	stomach
34	chr4:53707800-53709200	Enhancers	Right Atrium	heart
35	chr4:53707800-53709400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:53707800-53709600	Enhancers	Right Ventricle	heart
37	chr4:53707800-53709800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:53708000-53708600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:53708000-53708600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:53708000-53708600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:53708000-53708600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:53708000-53708600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr4:53708000-53708600	Enhancers	Esophagus	oesophagus
44	chr4:53708000-53708600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr4:53708000-53708600	Bivalent Enhancer	NHLF	lung
46	chr4:53708000-53709200	Enhancers	Fetal Muscle Trunk	muscle
47	chr4:53708000-53709400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:53708000-53709400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:53708000-53710000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:53708200-53708600	Flanking Active TSS	Adipose Nuclei	Adipose

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