Variant report

Variant	rs10054972
Chromosome Location	chr5:115175369-115175370
allele	C/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	CTCF	chr5:115175220-115175370	AG10803	skin:	n/a	n/a
2	CUX1	chr5:115174884-115175402	K562	blood:	n/a	n/a
3	RAD21	chr5:115174493-115175410	SK-N-SH	brain:	n/a	n/a
4	EBF1	chr5:115174764-115175439	GM12878	blood:	n/a	chr5:115175148-115175159
5	CTCF	chr5:115175220-115175370	HCM	heart:	n/a	n/a
6	CTCF	chr5:115175240-115175390	AG04450	lung:	n/a	n/a
7	CTCF	chr5:115174673-115176061	A549	lung:	n/a	n/a
8	ARID3A	chr5:115174740-115175480	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:115174756-115176043	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115169299..115172365-chr5:115175271..115177908,3	MCF-7	breast:
2	chr5:114959789..114964126-chr5:115174280..115179155,11	MCF-7	breast:

Variant related genes	Relation type
AP3S1	TF binding region
ATG12	TF binding region
ENSG00000145782	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000243414	Chromatin interaction
ENSG00000251201	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10036657	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10052079	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10058994	1.00[EUR][1000 genomes]
rs10059199	1.00[EUR][1000 genomes]
rs10067222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10070325	1.00[EUR][1000 genomes]
rs10074061	1.00[EUR][1000 genomes]
rs10074066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10075816	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10478262	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10519428	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519429	1.00[EUR][1000 genomes]
rs11959669	1.00[EUR][1000 genomes]
rs17138236	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1968365	1.00[EUR][1000 genomes]
rs28420368	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4920893	1.00[EUR][1000 genomes]
rs4921029	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4921030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861998	1.00[EUR][1000 genomes]
rs6872587	1.00[EUR][1000 genomes]
rs6875708	1.00[EUR][1000 genomes]
rs73257802	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73265480	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73265491	1.00[EUR][1000 genomes]
rs73780683	1.00[EUR][1000 genomes]
rs9326975	1.00[EUR][1000 genomes]
rs9654524	1.00[EUR][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	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 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	chr5:115161800-115176200	Weak transcription	Gastric	stomach
2	chr5:115162000-115176200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:115162000-115176600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:115162600-115175600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:115163000-115176400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:115166600-115175600	Weak transcription	Small Intestine	intestine
7	chr5:115168400-115176400	Weak transcription	Aorta	Aorta
8	chr5:115170400-115175600	Weak transcription	Right Ventricle	heart
9	chr5:115173400-115175400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:115173400-115175400	Weak transcription	HSMMtube	muscle
11	chr5:115173400-115176200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:115173400-115176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:115173800-115176200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr5:115174000-115175600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr5:115174000-115175800	Enhancers	Primary B cells from peripheral blood	blood
16	chr5:115174000-115176000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr5:115174000-115176000	Enhancers	Stomach Mucosa	stomach
18	chr5:115174000-115176000	Flanking Active TSS	HepG2	liver
19	chr5:115174000-115176200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr5:115174000-115176200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr5:115174000-115176200	Enhancers	Brain Substantia Nigra	brain
22	chr5:115174000-115176200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr5:115174200-115175400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:115174200-115175600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:115174200-115175800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:115174200-115176200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:115174200-115176200	Genic enhancers	Primary B cells from cord blood	blood
28	chr5:115174200-115176200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr5:115174200-115176600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:115174200-115176600	Flanking Active TSS	Dnd41	blood
31	chr5:115174400-115175400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:115174400-115175400	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr5:115174400-115176000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr5:115174400-115176000	Enhancers	Rectal Smooth Muscle	rectum
35	chr5:115174400-115176000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr5:115174400-115176200	Enhancers	Brain Angular Gyrus	brain
37	chr5:115174400-115176200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr5:115174400-115176200	Enhancers	Fetal Heart	heart
39	chr5:115174400-115176200	Enhancers	Fetal Lung	lung
40	chr5:115174400-115176200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr5:115174400-115176400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr5:115174400-115176600	Flanking Active TSS	Liver	Liver
43	chr5:115174400-115176600	Flanking Active TSS	HUVEC	blood vessel
44	chr5:115174600-115175400	Active TSS	NH-A	brain
45	chr5:115174600-115175800	Active TSS	Fetal Brain Female	brain
46	chr5:115174600-115175800	Enhancers	HSMM	muscle
47	chr5:115174600-115176000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr5:115174600-115176400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr5:115174600-115180000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:115174800-115175400	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links