Variant report

Variant	rs245577
Chromosome Location	chr5:14256589-14256590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14142719..14145389-chr5:14255713..14258192,4	MCF-7	breast:
2	chr5:14143210..14148732-chr5:14254944..14261067,10	MCF-7	breast:
3	chr5:14247745..14252723-chr5:14254933..14257114,4	MCF-7	breast:
4	chr5:14246723..14248369-chr5:14255798..14258024,2	MCF-7	breast:
5	chr5:14255845..14258384-chr5:14262309..14265414,3	MCF-7	breast:
6	chr5:14035881..14037914-chr5:14255980..14258485,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13175673	1.00[ASN][1000 genomes]
rs164861	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17302408	1.00[ASN][1000 genomes]
rs187125	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434605	1.00[ASN][1000 genomes]
rs2591277	0.99[EUR][1000 genomes]
rs2607077	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607078	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697663	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30616	1.00[ASN][1000 genomes]
rs30617	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30619	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30620	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354305	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354308	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39856	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42485	1.00[ASN][1000 genomes]
rs706271	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773701	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773702	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773763	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799025	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897724	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897726	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14247200-14256800	Weak transcription	Stomach Mucosa	stomach
2	chr5:14247400-14257000	Weak transcription	Gastric	stomach
3	chr5:14250800-14256800	Weak transcription	Ovary	ovary
4	chr5:14250800-14257000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:14251400-14257200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:14251800-14257200	Weak transcription	Brain Angular Gyrus	brain
7	chr5:14252000-14256800	Weak transcription	Fetal Stomach	stomach
8	chr5:14252000-14258200	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:14252200-14256800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:14252200-14257000	Weak transcription	Brain Germinal Matrix	brain
11	chr5:14252200-14257000	Weak transcription	Fetal Brain Female	brain
12	chr5:14252200-14257400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:14252400-14256800	Weak transcription	Fetal Brain Male	brain
14	chr5:14252400-14257600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:14252600-14256600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:14252600-14257200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:14252600-14257600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr5:14252600-14259000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:14252800-14257600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:14253000-14257000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:14253000-14257000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:14253000-14257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:14253000-14257600	ZNF genes & repeats	GM12878-XiMat	blood
24	chr5:14253000-14258200	Weak transcription	Pancreas	Pancrea
25	chr5:14253000-14258400	Weak transcription	Brain Substantia Nigra	brain
26	chr5:14253200-14256800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:14253200-14257000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:14253200-14257000	Weak transcription	Brain Anterior Caudate	brain
29	chr5:14253200-14257000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:14253800-14257200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr5:14253800-14257400	ZNF genes & repeats	HSMM	muscle
32	chr5:14253800-14264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:14254000-14261400	Weak transcription	Thymus	Thymus
34	chr5:14254600-14256800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:14254600-14257000	ZNF genes & repeats	NH-A	brain
36	chr5:14254600-14257200	ZNF genes & repeats	NHLF	lung
37	chr5:14254600-14257400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:14254600-14258200	ZNF genes & repeats	A549	lung
39	chr5:14255000-14256800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:14255000-14256800	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:14255000-14257400	ZNF genes & repeats	NHEK	skin
42	chr5:14255200-14257000	ZNF genes & repeats	NHDF-Ad	bronchial
43	chr5:14255200-14257000	Strong transcription	Osteobl	bone
44	chr5:14255200-14257400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:14255200-14257600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
46	chr5:14255400-14256600	Weak transcription	Adipose Nuclei	Adipose
47	chr5:14255400-14256800	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:14255400-14257000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr5:14255400-14257200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:14255400-14260400	Enhancers	Skeletal Muscle Female	skeletal muscle

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