Variant report

Variant	rs17236219
Chromosome Location	chr5:68669939-68669940
allele	C/G
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	CUX1	chr5:68669806-68669972	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68663499..68666759-chr5:68669120..68673475,5	MCF-7	breast:
2	chr5:68669176..68671492-chr5:68672021..68673716,2	MCF-7	breast:

Variant related genes	Relation type
TAF9	TF binding region
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs17236380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17236618	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17236639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4252222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4252226	1.00[EUR][1000 genomes]
rs4252229	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55754329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55764482	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56112110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56362385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57344277	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57402724	1.00[EUR][1000 genomes]
rs57714822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58172827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58381452	1.00[EUR][1000 genomes]
rs58742544	1.00[EUR][1000 genomes]
rs59233462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59776629	1.00[EUR][1000 genomes]
rs59799008	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60644166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61244656	1.00[EUR][1000 genomes]
rs61290150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861518	1.00[EUR][1000 genomes]
rs6876889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772537	1.00[AMR][1000 genomes]
rs73772541	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772544	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772545	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7725200	1.00[EUR][1000 genomes]
rs8192269	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68666200-68672800	Weak transcription	Small Intestine	intestine
2	chr5:68666200-68678000	Weak transcription	Spleen	Spleen
3	chr5:68666600-68670400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:68666600-68670600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:68666600-68670600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:68666600-68670600	Weak transcription	HSMMtube	muscle
7	chr5:68666600-68671200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:68666600-68671600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:68666600-68671800	Weak transcription	Ovary	ovary
10	chr5:68666600-68672600	Weak transcription	Left Ventricle	heart
11	chr5:68666600-68677800	Weak transcription	Colonic Mucosa	Colon
12	chr5:68666600-68677800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:68666600-68681000	Weak transcription	Lung	lung
14	chr5:68666600-68689600	Weak transcription	Aorta	Aorta
15	chr5:68666600-68689800	Weak transcription	Gastric	stomach
16	chr5:68666600-68689800	Weak transcription	Right Ventricle	heart
17	chr5:68666600-68696200	Weak transcription	Pancreas	Pancrea
18	chr5:68666600-68705000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:68666600-68710800	Weak transcription	Esophagus	oesophagus
20	chr5:68666800-68670400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:68666800-68670400	Weak transcription	Fetal Thymus	thymus
22	chr5:68666800-68670400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:68666800-68670600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:68666800-68670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:68666800-68670600	Weak transcription	Brain Angular Gyrus	brain
26	chr5:68666800-68670600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:68666800-68670600	Weak transcription	Brain Substantia Nigra	brain
28	chr5:68666800-68670600	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:68666800-68670800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:68666800-68670800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:68666800-68671000	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:68666800-68671800	Enhancers	Primary B cells from peripheral blood	blood
33	chr5:68666800-68672200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:68666800-68672600	Weak transcription	Fetal Stomach	stomach
35	chr5:68666800-68676600	Weak transcription	Thymus	Thymus
36	chr5:68666800-68677800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:68666800-68677800	Weak transcription	Fetal Kidney	kidney
38	chr5:68666800-68710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:68666800-68710600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:68666800-68710800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:68666800-68710800	Weak transcription	Psoas Muscle	Psoas
42	chr5:68667000-68670400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:68667000-68670400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:68667000-68670400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:68667000-68670400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:68667000-68670400	Weak transcription	Adipose Nuclei	Adipose
47	chr5:68667000-68670400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:68667000-68670600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr5:68667000-68670600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:68667000-68670600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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