Variant report

Variant	rs57559233
Chromosome Location	chr5:177551607-177551608
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:177539929..177541051-chr5:177551226..177551840,3	MCF-7	breast:
2	chr17:57920673..57923074-chr5:177550900..177553018,2	MCF-7	breast:
3	chr5:177504960..177505907-chr5:177550881..177551952,4	MCF-7	breast:
4	chr5:177502921..177503789-chr5:177551262..177552086,2	MCF-7	breast:
5	chr5:177548762..177553216-chr5:177630602..177633012,4	MCF-7	breast:
6	chr5:177551220..177552161-chr5:177572718..177573791,3	MCF-7	breast:
7	chr5:177543096..177543972-chr5:177550978..177551700,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145916	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000145911	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11951603	1.00[AMR][1000 genomes]
rs57947175	1.00[AMR][1000 genomes]
rs59922179	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60772567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61577981	1.00[AMR][1000 genomes]
rs73338853	1.00[AMR][1000 genomes]
rs73348139	1.00[AMR][1000 genomes]
rs73348150	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73348160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73348162	0.87[AFR][1000 genomes]
rs73348167	0.87[AFR][1000 genomes]
rs73348177	1.00[AMR][1000 genomes]
rs73348182	1.00[AMR][1000 genomes]
rs73348185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73348192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73348194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73348199	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73349806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73349889	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73351244	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
3	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
5	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
9	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv883191	chr5:177535370-177551985	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv883192	chr5:177535370-177564346	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177541800-177557200	Weak transcription	Right Atrium	heart
2	chr5:177544600-177552200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:177545200-177552000	Enhancers	Fetal Thymus	thymus
4	chr5:177546200-177551800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
5	chr5:177546200-177552000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:177546400-177552200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:177547000-177553400	Weak transcription	HUVEC	blood vessel
8	chr5:177548600-177557000	Weak transcription	Fetal Intestine Large	intestine
9	chr5:177548800-177557000	Weak transcription	Fetal Intestine Small	intestine
10	chr5:177548800-177557200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:177549000-177552200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:177549200-177552800	Genic enhancers	Fetal Stomach	stomach
13	chr5:177549200-177553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:177549400-177552800	Genic enhancers	Fetal Muscle Leg	muscle
15	chr5:177549400-177553000	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr5:177549400-177554800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:177549400-177557200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:177549400-177558200	Weak transcription	Fetal Heart	heart
19	chr5:177549600-177551800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
20	chr5:177549600-177557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:177549600-177557200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:177549600-177557400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:177549800-177553400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:177550000-177552000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr5:177550000-177553400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:177550200-177551800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:177550200-177552200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:177550200-177552400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:177550200-177552400	Enhancers	Lung	lung
30	chr5:177550200-177553600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:177550200-177554600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr5:177550200-177557000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:177550400-177551800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:177550400-177552800	Enhancers	Esophagus	oesophagus
35	chr5:177550400-177556400	Weak transcription	GM12878-XiMat	blood
36	chr5:177550400-177557200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:177550600-177551800	Enhancers	Spleen	Spleen
38	chr5:177550600-177552000	Enhancers	Stomach Mucosa	stomach
39	chr5:177550600-177552200	Enhancers	Fetal Lung	lung
40	chr5:177550600-177553600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:177550600-177553800	Weak transcription	Left Ventricle	heart
42	chr5:177550600-177557200	Weak transcription	Psoas Muscle	Psoas
43	chr5:177550800-177551800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr5:177550800-177552200	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr5:177550800-177552200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:177550800-177553600	Enhancers	K562	blood
47	chr5:177550800-177556800	Weak transcription	Primary B cells from cord blood	blood
48	chr5:177551000-177552000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:177551000-177552000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr5:177551000-177552200	Enhancers	Gastric	stomach

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