Variant report

Variant	rs7660342
Chromosome Location	chr4:53706678-53706679
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53705671..53708824-chr4:53710798..53715308,4	MCF-7	breast:
2	chr4:53576916..53581689-chr4:53705110..53710230,9	MCF-7	breast:
3	chr4:53587084..53590122-chr4:53703500..53706827,4	MCF-7	breast:

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

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1109696	1.00[ASN][1000 genomes]
rs17698482	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699414	1.00[ASN][1000 genomes]
rs2007936	1.00[ASN][1000 genomes]
rs2007959	1.00[ASN][1000 genomes]
rs6554055	0.81[EUR][1000 genomes]
rs73250906	1.00[ASN][1000 genomes]
rs73250912	1.00[ASN][1000 genomes]
rs7662817	0.81[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	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	chr4:53701000-53706800	Weak transcription	Stomach Mucosa	stomach
5	chr4:53701000-53707000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:53701000-53707800	Weak transcription	Aorta	Aorta
7	chr4:53702400-53707200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:53702400-53709200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr4:53702400-53709800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:53703000-53707400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:53703200-53708200	Weak transcription	Fetal Kidney	kidney
12	chr4:53703600-53707600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:53703800-53707800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr4:53703800-53709000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr4:53704000-53709200	Enhancers	Psoas Muscle	Psoas
16	chr4:53704000-53709200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:53704000-53709400	Enhancers	Fetal Heart	heart
18	chr4:53704000-53709600	Enhancers	Left Ventricle	heart
19	chr4:53704000-53710000	Enhancers	Fetal Muscle Leg	muscle
20	chr4:53704200-53706800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:53704200-53709800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:53704400-53708200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:53704600-53707400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:53704600-53709400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:53704800-53707000	Enhancers	Brain Germinal Matrix	brain
26	chr4:53705000-53707800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:53705000-53707800	Weak transcription	Gastric	stomach
28	chr4:53705000-53708200	Weak transcription	Fetal Intestine Small	intestine
29	chr4:53705000-53708400	Enhancers	HMEC	breast
30	chr4:53705000-53709400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:53705200-53706800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:53705200-53706800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:53705200-53707600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:53705200-53707800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:53705200-53707800	Weak transcription	Pancreas	Pancrea
36	chr4:53705200-53708000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:53705200-53708000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:53705200-53708000	Weak transcription	Esophagus	oesophagus
39	chr4:53705200-53708200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:53705400-53707400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:53705400-53707600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:53705600-53706800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:53705600-53706800	Weak transcription	HSMMtube	muscle
44	chr4:53705600-53707400	Weak transcription	Brain Substantia Nigra	brain
45	chr4:53705600-53707800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:53705600-53707800	Weak transcription	NH-A	brain
47	chr4:53705600-53707800	Enhancers	NHEK	skin
48	chr4:53705600-53708000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:53705600-53708000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:53705800-53706800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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