Variant report

Variant	rs55920097
Chromosome Location	chr5:179281315-179281316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179280399..179282858-chr5:179283698..179286388,4	K562	blood:
2	chr5:179231147..179233886-chr5:179278531..179282466,3	MCF-7	breast:
3	chr5:179279889..179282788-chr5:179478192..179480009,2	K562	blood:
4	chr5:179247658..179250130-chr5:179280236..179282871,2	K562	blood:
5	chr5:179185963..179187544-chr5:179278623..179281522,2	K562	blood:
6	chr5:179275469..179281873-chr5:179283079..179286385,9	MCF-7	breast:
7	chr5:179231868..179233837-chr5:179281253..179282818,2	MCF-7	breast:
8	chr5:179280059..179282824-chr5:179286151..179287699,2	K562	blood:
9	chr5:179267574..179269837-chr5:179280318..179284671,3	MCF-7	breast:
10	chr5:179272936..179275402-chr5:179280139..179282977,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245317	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000252202	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs269456	0.94[AFR][1000 genomes]
rs269462	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs375186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs437806	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57322113	1.00[EUR][1000 genomes]
rs60356119	0.92[EUR][1000 genomes]
rs66959508	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881038	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6883240	1.00[EUR][1000 genomes]
rs6883858	1.00[EUR][1000 genomes]
rs72813738	1.00[EUR][1000 genomes]
rs72813740	1.00[EUR][1000 genomes]
rs7709069	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179264600-179285000	Weak transcription	Psoas Muscle	Psoas
2	chr5:179265000-179285000	Weak transcription	Stomach Mucosa	stomach
3	chr5:179274000-179284000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:179274200-179281600	Strong transcription	Fetal Stomach	stomach
5	chr5:179274600-179285000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:179275800-179285000	Weak transcription	Fetal Heart	heart
7	chr5:179278000-179284200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:179278000-179284600	Weak transcription	NH-A	brain
9	chr5:179278200-179283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:179278200-179284600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:179278200-179284600	Weak transcription	HMEC	breast
12	chr5:179278200-179284600	Weak transcription	NHEK	skin
13	chr5:179278200-179285000	Weak transcription	Fetal Kidney	kidney
14	chr5:179278200-179285000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:179278200-179285000	Weak transcription	HUVEC	blood vessel
16	chr5:179278400-179284600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:179278600-179284600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:179278800-179284600	Weak transcription	Hela-S3	cervix
19	chr5:179278800-179285000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:179278800-179285000	Weak transcription	Small Intestine	intestine
21	chr5:179279800-179284600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:179280000-179284600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:179280000-179284600	Weak transcription	K562	blood
24	chr5:179280000-179284600	Weak transcription	NHLF	lung
25	chr5:179280000-179285000	Weak transcription	Placenta	Placenta
26	chr5:179280200-179281400	Weak transcription	Osteobl	bone
27	chr5:179280200-179284400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:179280200-179284400	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:179280200-179284600	Weak transcription	Brain Substantia Nigra	brain
30	chr5:179280200-179284600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:179280200-179284600	Weak transcription	HSMMtube	muscle
32	chr5:179280200-179285000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:179280200-179285000	Weak transcription	Aorta	Aorta
34	chr5:179280200-179285000	Weak transcription	Colonic Mucosa	Colon
35	chr5:179280200-179285000	Weak transcription	Esophagus	oesophagus
36	chr5:179280200-179285000	Weak transcription	Pancreas	Pancrea
37	chr5:179280200-179285000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:179280400-179281400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:179280400-179281400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:179280400-179282200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:179280400-179282600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:179280400-179283200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:179280400-179283200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:179280400-179283200	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:179280400-179283400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:179280400-179283400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:179280400-179283400	Weak transcription	Brain Germinal Matrix	brain
48	chr5:179280400-179283400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:179280400-179283400	Weak transcription	Ovary	ovary
50	chr5:179280400-179283800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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