Variant report

Variant	rs6883858
Chromosome Location	chr5:179277088-179277089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179270819..179273884-chr5:179274460..179277805,3	MCF-7	breast:
2	chr5:179275469..179281873-chr5:179283079..179286385,9	MCF-7	breast:
3	chr5:179228970..179231502-chr5:179276172..179278068,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222448	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000245317	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs269462	1.00[EUR][1000 genomes]
rs375186	0.96[EUR][1000 genomes]
rs437806	0.92[EUR][1000 genomes]
rs55920097	1.00[EUR][1000 genomes]
rs57322113	1.00[EUR][1000 genomes]
rs60356119	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66959508	1.00[EUR][1000 genomes]
rs6881038	0.88[EUR][1000 genomes]
rs6883240	1.00[EUR][1000 genomes]
rs72813738	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813740	1.00[EUR][1000 genomes]
rs7709069	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	chr5:179262600-179279400	Strong transcription	Brain Inferior Temporal Lobe	brain
2	chr5:179263000-179279600	Strong transcription	Brain Anterior Caudate	brain
3	chr5:179263000-179279800	Strong transcription	Brain Hippocampus Middle	brain
4	chr5:179263000-179280400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:179263600-179280200	Strong transcription	Colon Smooth Muscle	Colon
6	chr5:179264600-179285000	Weak transcription	Psoas Muscle	Psoas
7	chr5:179265000-179285000	Weak transcription	Stomach Mucosa	stomach
8	chr5:179266400-179277200	Weak transcription	HMEC	breast
9	chr5:179267000-179277600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:179268200-179280600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:179270600-179279800	Strong transcription	Brain Cingulate Gyrus	brain
12	chr5:179270600-179280200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:179270600-179280400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:179270800-179280200	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:179270800-179280600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:179271000-179280400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:179271000-179280400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:179271400-179280400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:179272400-179280400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:179272400-179280400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:179272400-179280400	Strong transcription	Fetal Intestine Large	intestine
22	chr5:179272400-179280600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:179272600-179280200	Strong transcription	Pancreas	Pancrea
24	chr5:179272600-179280400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr5:179272600-179280400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:179272600-179280400	Strong transcription	Left Ventricle	heart
27	chr5:179272600-179280400	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:179272600-179280600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:179272800-179278200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr5:179272800-179278400	Strong transcription	Liver	Liver
31	chr5:179272800-179278400	Strong transcription	Lung	lung
32	chr5:179272800-179278600	Strong transcription	Spleen	Spleen
33	chr5:179272800-179279600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:179272800-179280200	Strong transcription	HSMMtube	muscle
35	chr5:179272800-179280400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:179272800-179280400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:179272800-179280400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr5:179272800-179280400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:179272800-179280400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:179272800-179280400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:179272800-179280400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:179272800-179280400	Strong transcription	Ovary	ovary
43	chr5:179272800-179280400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr5:179272800-179280400	Strong transcription	NHDF-Ad	bronchial
45	chr5:179273000-179278400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:179273000-179278400	Strong transcription	GM12878-XiMat	blood
47	chr5:179273000-179279600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:179273000-179280200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:179273000-179280200	Strong transcription	Osteobl	bone
50	chr5:179273000-179280400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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