Variant report

Variant	rs72824554
Chromosome Location	chr5:179055449-179055450
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179044238..179046720-chr5:179054940..179057322,2	MCF-7	breast:
2	chr5:179054324..179056626-chr5:179057842..179060388,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10479544	0.84[ASN][1000 genomes]
rs11958537	0.82[ASN][1000 genomes]
rs12188476	1.00[ASN][1000 genomes]
rs12514650	0.88[ASN][1000 genomes]
rs12518041	1.00[ASN][1000 genomes]
rs12519803	1.00[ASN][1000 genomes]
rs17355294	1.00[ASN][1000 genomes]
rs28533619	0.83[ASN][1000 genomes]
rs4128628	1.00[ASN][1000 genomes]
rs4128629	1.00[ASN][1000 genomes]
rs4535419	1.00[ASN][1000 genomes]
rs4701133	0.83[ASN][1000 genomes]
rs55696570	0.85[ASN][1000 genomes]
rs55741920	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55821473	1.00[ASN][1000 genomes]
rs55837909	0.82[ASN][1000 genomes]
rs56198018	0.83[ASN][1000 genomes]
rs56370020	0.92[ASN][1000 genomes]
rs58788190	1.00[ASN][1000 genomes]
rs60104959	1.00[ASN][1000 genomes]
rs61408162	1.00[ASN][1000 genomes]
rs62392796	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6874476	0.85[ASN][1000 genomes]
rs7442819	0.95[ASN][1000 genomes]
rs7706115	0.83[ASN][1000 genomes]
rs7710813	0.83[ASN][1000 genomes]
rs7715391	0.84[ASN][1000 genomes]
rs7732888	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
4	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv883273	chr5:179045142-179086833	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
6	nsv823357	chr5:179046318-179058193	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179051600-179060600	Weak transcription	Ovary	ovary
2	chr5:179051800-179060600	Weak transcription	Fetal Kidney	kidney
3	chr5:179052000-179058200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:179052000-179061400	Weak transcription	Spleen	Spleen
5	chr5:179052200-179055800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:179052200-179056200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:179052200-179056200	Weak transcription	Fetal Intestine Small	intestine
8	chr5:179052200-179058800	Weak transcription	Pancreas	Pancrea
9	chr5:179052200-179059000	Weak transcription	Fetal Intestine Large	intestine
10	chr5:179052200-179059200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:179052200-179059200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:179052200-179059200	Weak transcription	Fetal Stomach	stomach
13	chr5:179052200-179059400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179052200-179059400	Weak transcription	Fetal Thymus	thymus
15	chr5:179052200-179059400	Weak transcription	Lung	lung
16	chr5:179052200-179059400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:179052200-179060200	Weak transcription	Stomach Mucosa	stomach
18	chr5:179052200-179060400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:179052200-179060400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:179052200-179060600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:179052200-179060600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:179052200-179060600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:179052200-179060600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:179052200-179060600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:179052200-179060600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:179052200-179060600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:179052200-179060600	Weak transcription	Adipose Nuclei	Adipose
28	chr5:179052200-179060600	Weak transcription	Brain Anterior Caudate	brain
29	chr5:179052200-179060600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:179052200-179060600	Weak transcription	Brain Germinal Matrix	brain
31	chr5:179052200-179060600	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:179052200-179060600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr5:179052200-179060600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:179052200-179060600	Weak transcription	Esophagus	oesophagus
35	chr5:179052200-179060600	Weak transcription	Fetal Brain Female	brain
36	chr5:179052200-179060600	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:179052200-179060600	Weak transcription	Gastric	stomach
38	chr5:179052200-179060600	Weak transcription	Left Ventricle	heart
39	chr5:179052200-179060600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr5:179052200-179060600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:179052200-179060600	Weak transcription	Right Ventricle	heart
42	chr5:179052200-179060600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:179052200-179060600	Weak transcription	HMEC	breast
44	chr5:179052200-179060600	Weak transcription	HSMM	muscle
45	chr5:179052200-179060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr5:179052200-179060800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr5:179052200-179085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:179052400-179059400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:179052400-179059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:179052400-179059400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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