Variant report

Variant	rs28655678
Chromosome Location	chr5:179340714-179340715
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179339757..179341423-chr5:179384531..179387426,2	MCF-7	breast:
2	chr5:179333591..179336519-chr5:179336661..179341628,9	MCF-7	breast:
3	chr5:179333496..179336752-chr5:179337888..179342042,8	K562	blood:
4	chr5:179339541..179342239-chr5:179346452..179348060,2	K562	blood:

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10054440	1.00[EUR][1000 genomes]
rs10065641	1.00[AFR][1000 genomes]
rs10069416	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10070019	1.00[EUR][1000 genomes]
rs10479551	0.86[AFR][1000 genomes]
rs12513658	1.00[EUR][1000 genomes]
rs13436232	1.00[EUR][1000 genomes]
rs2099043	1.00[EUR][1000 genomes]
rs28723449	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
3	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
4	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
6	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
7	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179335200-179343000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:179335200-179343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:179335400-179340800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:179335400-179344200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:179335400-179344400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:179335400-179344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:179335400-179346400	Weak transcription	Brain Angular Gyrus	brain
8	chr5:179335400-179346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179335600-179340800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:179335600-179344200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:179335800-179340800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:179335800-179340800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:179335800-179340800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:179335800-179340800	Weak transcription	Osteobl	bone
15	chr5:179335800-179341000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:179335800-179341000	Weak transcription	Brain Substantia Nigra	brain
17	chr5:179335800-179358200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:179336000-179340800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:179336000-179341000	Weak transcription	Lung	lung
20	chr5:179336000-179344200	Weak transcription	Primary B cells from cord blood	blood
21	chr5:179336000-179346200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:179336000-179349000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:179336000-179361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:179336200-179340800	Weak transcription	Placenta	Placenta
25	chr5:179336200-179341000	Weak transcription	Adipose Nuclei	Adipose
26	chr5:179336400-179340800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr5:179336600-179341000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:179339200-179341800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr5:179339400-179340800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr5:179339400-179340800	Enhancers	Stomach Mucosa	stomach
31	chr5:179339400-179340800	Enhancers	Stomach Smooth Muscle	stomach
32	chr5:179339400-179341600	Enhancers	Gastric	stomach
33	chr5:179339400-179342000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr5:179339400-179342000	Strong transcription	Brain Germinal Matrix	brain
35	chr5:179339600-179340800	Enhancers	Fetal Brain Male	brain
36	chr5:179339600-179341600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:179339600-179341600	Enhancers	Esophagus	oesophagus
38	chr5:179339800-179340800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:179339800-179340800	Enhancers	HSMMtube	muscle
40	chr5:179339800-179341000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr5:179339800-179341600	Enhancers	HMEC	breast
42	chr5:179340000-179340800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr5:179340000-179341000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr5:179340000-179341600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:179340000-179341600	Enhancers	Colonic Mucosa	Colon
46	chr5:179340000-179341800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:179340200-179341200	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:179340200-179341200	Weak transcription	Fetal Brain Female	brain
49	chr5:179340400-179341400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr5:179340400-179341800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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