Variant report

Variant	rs28599770
Chromosome Location	chr5:115231390-115231391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115231047..115233033-chr5:115237062..115238617,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10052982	0.84[EUR][1000 genomes]
rs10056468	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10063812	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10071790	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10519432	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11241339	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62371475	0.82[AMR][1000 genomes]
rs62371492	0.90[EUR][1000 genomes]
rs62371493	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6594909	0.84[EUR][1000 genomes]
rs9326977	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3401617	chr5:115205732-115238678	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1021968	chr5:115213162-115426468	Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv462400	chr5:115223504-115428381	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv599478	chr5:115223504-115428381	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	esv3441679	chr5:115230797-115238631	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 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	chr5:115189800-115235800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr5:115193200-115239000	Weak transcription	Gastric	stomach
3	chr5:115193600-115234600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:115195400-115263200	Weak transcription	Aorta	Aorta
5	chr5:115196000-115233600	Weak transcription	Esophagus	oesophagus
6	chr5:115203400-115233400	Weak transcription	Fetal Brain Male	brain
7	chr5:115205600-115254200	Weak transcription	Small Intestine	intestine
8	chr5:115207600-115233600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:115207600-115238400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:115207600-115239200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:115207600-115244600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:115207600-115253800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:115207600-115254600	Weak transcription	Fetal Kidney	kidney
14	chr5:115207800-115250800	Weak transcription	Adipose Nuclei	Adipose
15	chr5:115207800-115254000	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:115208000-115253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:115208200-115236000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:115208600-115235600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr5:115209200-115234200	Weak transcription	HSMM	muscle
20	chr5:115209400-115232600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:115209800-115234000	Weak transcription	HUVEC	blood vessel
22	chr5:115212000-115236000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:115212600-115238200	Weak transcription	Dnd41	blood
24	chr5:115217800-115234000	Weak transcription	GM12878-XiMat	blood
25	chr5:115218600-115253000	Weak transcription	Placenta	Placenta
26	chr5:115218800-115253600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:115219000-115252800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:115219200-115233600	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:115219200-115234000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:115219200-115252800	Weak transcription	Pancreas	Pancrea
31	chr5:115219200-115253200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:115219400-115233600	Weak transcription	Primary T cells from cord blood	blood
33	chr5:115219400-115234000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:115219400-115234200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:115219400-115234200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:115219400-115234200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:115219400-115234400	Weak transcription	Left Ventricle	heart
38	chr5:115219400-115236200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:115219400-115246800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:115219400-115251000	Weak transcription	Fetal Lung	lung
41	chr5:115219400-115252600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:115219600-115231400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:115219600-115256000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:115221400-115253800	Weak transcription	Fetal Stomach	stomach
45	chr5:115221400-115254400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:115222000-115252800	Weak transcription	Fetal Intestine Small	intestine
47	chr5:115222200-115233200	Weak transcription	Fetal Intestine Large	intestine
48	chr5:115225000-115233000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:115225400-115234000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:115225600-115253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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