Variant report

Variant	rs17882279
Chromosome Location	chr5:79379511-79379512
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr5:79379407-79379689	K562	blood:	n/a	n/a
2	RAD21	chr5:79378665-79379730	GM12878	blood:	n/a	chr5:79378805-79378824
3	CTCF	chr5:79379480-79379630	BE2_C	brain:	n/a	n/a
4	CTCF	chr5:79379380-79379530	HVMF	connective:	n/a	n/a
5	CTCF	chr5:79379440-79379590	HRPEpiC	eye:	n/a	n/a
6	SMC3	chr5:79379301-79379723	HepG2	liver:	n/a	n/a
7	CTCF	chr5:79379420-79379570	HCT-116	colon:	n/a	n/a
8	CTCF	chr5:79379310-79379682	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr5:79379277-79379737	HepG2	liver:	n/a	n/a
10	CTCF	chr5:79379420-79379680	Lung_OC	lung:	n/a	n/a
11	CTCF	chr5:79379445-79379533	ProgFib	skin:	n/a	n/a
12	CTCF	chr5:79379420-79379570	HEK293	kidney:	n/a	n/a
13	CTCF	chr5:79379400-79379550	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr5:79379440-79379590	HEEpiC	esophagus:	n/a	n/a
15	CTCF	chr5:79379480-79379630	Caco-2	colon:	n/a	n/a
16	CTCF	chr5:79379375-79379650	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr5:79379420-79379570	GM12864	blood:	n/a	n/a
18	CTCF	chr5:79379303-79379687	ECC-1	luminal epithelium:	n/a	n/a
19	FOXA1	chr5:79379391-79379697	T-47D	breast:	n/a	n/a
20	RAD21	chr5:79379310-79379561	K562	blood:	n/a	n/a
21	CTCF	chr5:79379420-79379570	HRE	kidney:	n/a	n/a
22	CTCF	chr5:79379409-79379660	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr5:79379253-79379751	HepG2	liver:	n/a	n/a
24	CTCF	chr5:79379440-79379590	AG10803	skin:	n/a	n/a
25	CTCF	chr5:79379420-79379570	SAEC	small airway:	n/a	n/a
26	CTCF	chr5:79379440-79379590	GM12865	blood:	n/a	n/a
27	CTCF	chr5:79379420-79379570	GM12865	blood:	n/a	n/a
28	RAD21	chr5:79378448-79379832	HCT-116	colon:	n/a	chr5:79378805-79378824
29	CTCF	chr5:79379400-79379550	BE2_C	brain:	n/a	n/a
30	MYC	chr5:79378755-79379635	MCF10A-Er-Src	breast:	n/a	chr5:79379132-79379141 chr5:79379131-79379142 chr5:79378834-79378844
31	CTCF	chr5:79379460-79379610	HA-sp	spinal cord:	n/a	n/a
32	CTCF	chr5:79379500-79379650	HL-60	blood:	n/a	n/a
33	CTCF	chr5:79379380-79379530	HAc	cerebellar:	n/a	n/a
34	E2F4	chr5:79379378-79379664	MCF10A-Er-Src	breast:	n/a	n/a
35	CTCF	chr5:79379460-79379610	GM12872	blood:	n/a	n/a
36	RAD21	chr5:79379431-79379624	K562	blood:	n/a	n/a
37	RAD21	chr5:79379312-79379753	Hela-S3	cervix:	n/a	n/a
38	TEAD4	chr5:79379291-79379787	HepG2	liver:	n/a	n/a
39	RAD21	chr5:79379224-79379789	A549	lung:	n/a	n/a
40	CTCF	chr5:79379440-79379590	AG04450	lung:	n/a	n/a
41	RAD21	chr5:79379157-79379748	SK-N-SH_RA	brain:	n/a	n/a
42	SMC3	chr5:79379316-79379707	K562	blood:	n/a	n/a
43	CTCF	chr5:79379480-79379630	HCM	heart:	n/a	n/a
44	FOXA1	chr5:79379407-79379747	HepG2	liver:	n/a	n/a
45	CTCF	chr5:79379430-79379654	GM10248	blood:	n/a	n/a
46	CTCF	chr5:79379440-79379590	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr5:79379407-79379667	A549	lung:	n/a	n/a
48	CTCF	chr5:79379420-79379570	GM12874	blood:	n/a	n/a
49	MAX	chr5:79379261-79379621	NB4	blood:	n/a	n/a
50	CTCF	chr5:79378607-79379826	GM12878	blood:	n/a	chr5:79378809-79378822 chr5:79378802-79378823 chr5:79378807-79378825 chr5:79378808-79378824

Variant related genes	Relation type
ENSG00000249825	TF binding region

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10462572	0.86[EUR][1000 genomes]
rs12110039	0.85[EUR][1000 genomes]
rs12186362	0.86[EUR][1000 genomes]
rs12188015	0.86[EUR][1000 genomes]
rs12523107	0.94[EUR][1000 genomes]
rs12523112	0.92[EUR][1000 genomes]
rs17880343	0.90[AMR][1000 genomes]
rs2118732	0.91[EUR][1000 genomes]
rs62363982	0.86[EUR][1000 genomes]
rs6453500	0.86[EUR][1000 genomes]
rs6453501	0.86[EUR][1000 genomes]
rs6891246	0.83[EUR][1000 genomes]
rs7707343	0.82[EUR][1000 genomes]
rs7725944	0.86[EUR][1000 genomes]
rs7736549	0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79366000-79388000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:79366200-79385000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:79366200-79392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:79374800-79381800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:79378000-79379600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr5:79378200-79385000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:79378400-79379600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:79378400-79379600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:79378400-79379600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:79378400-79379600	Enhancers	Liver	Liver
11	chr5:79378600-79379600	Active TSS	A549	lung
12	chr5:79378800-79379600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:79378800-79379600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr5:79378800-79379600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr5:79378800-79379600	Active TSS	Stomach Smooth Muscle	stomach
16	chr5:79378800-79379600	Active TSS	K562	blood
17	chr5:79379000-79379600	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr5:79379000-79379600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr5:79379200-79379600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr5:79379200-79379600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:79379200-79379600	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr5:79379200-79379600	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr5:79379200-79379600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr5:79379200-79379600	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr5:79379200-79379600	Enhancers	Pancreas	Pancrea
26	chr5:79379400-79379600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:79379400-79379600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:79379400-79379600	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr5:79379400-79379600	Active TSS	Primary B cells from cord blood	blood
30	chr5:79379400-79379600	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:79379400-79379600	Enhancers	Primary T cells from cord blood	blood
32	chr5:79379400-79379600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr5:79379400-79379600	Active TSS	Primary hematopoietic stem cells	blood
34	chr5:79379400-79379600	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr5:79379400-79379600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr5:79379400-79379600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:79379400-79379600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr5:79379400-79379600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:79379400-79379600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:79379400-79379600	Active TSS	Brain Angular Gyrus	brain
41	chr5:79379400-79379600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:79379400-79379600	Enhancers	Fetal Muscle Leg	muscle
43	chr5:79379400-79379600	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr5:79379400-79379600	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr5:79379400-79379600	Enhancers	NHLF	lung
46	chr5:79379400-79379800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:79379400-79380000	Enhancers	Brain Substantia Nigra	brain
48	chr5:79379400-79380600	Weak transcription	HepG2	liver
49	chr5:79379400-79381200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:79379400-79381600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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