Variant report

Variant	rs2454193
Chromosome Location	chr1:179712616-179712617
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179712115..179713115-chr7:100486907..100487582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176125	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1052447	0.89[ASN][1000 genomes]
rs10798718	0.89[ASN][1000 genomes]
rs10798719	0.88[ASN][1000 genomes]
rs10798720	0.88[ASN][1000 genomes]
rs10798721	0.88[ASN][1000 genomes]
rs10913874	0.89[ASN][1000 genomes]
rs10913876	0.89[ASN][1000 genomes]
rs10913877	0.89[ASN][1000 genomes]
rs10913878	0.89[ASN][1000 genomes]
rs10913879	0.88[ASN][1000 genomes]
rs12047821	0.88[ASN][1000 genomes]
rs12408874	0.89[ASN][1000 genomes]
rs12408882	0.89[ASN][1000 genomes]
rs2245195	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2318389	0.89[ASN][1000 genomes]
rs2454195	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2454196	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2487739	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487740	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2504039	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2504040	0.89[ASN][1000 genomes]
rs2504041	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2504042	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2504053	0.82[ASN][1000 genomes]
rs3845381	0.89[ASN][1000 genomes]
rs3845382	0.85[ASN][1000 genomes]
rs3845383	0.84[ASN][1000 genomes]
rs3856045	0.89[ASN][1000 genomes]
rs3909014	0.88[ASN][1000 genomes]
rs3909015	0.89[ASN][1000 genomes]
rs4269737	0.80[ASN][1000 genomes]
rs4469684	0.89[ASN][1000 genomes]
rs4511077	0.89[ASN][1000 genomes]
rs4651050	0.86[ASN][1000 genomes]
rs60556788	0.86[ASN][1000 genomes]
rs61828370	0.88[ASN][1000 genomes]
rs6663482	0.89[ASN][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	nsv548339	chr1:179686244-179722827	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179711400-179714400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:179711600-179713200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
3	chr1:179711600-179713200	Bivalent Enhancer	Fetal Lung	lung
4	chr1:179711600-179713400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:179711600-179713600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:179711600-179713800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:179711600-179713800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:179711600-179713800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
9	chr1:179711600-179714000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr1:179711600-179714000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:179711800-179712800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:179711800-179713000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:179711800-179713200	Active TSS	Right Atrium	heart
14	chr1:179711800-179713400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
15	chr1:179711800-179713400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr1:179711800-179713600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:179711800-179713600	Bivalent Enhancer	Spleen	Spleen
18	chr1:179711800-179713800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:179711800-179713800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr1:179711800-179713800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:179711800-179713800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
22	chr1:179711800-179714000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:179711800-179714000	Bivalent Enhancer	Placenta	Placenta
24	chr1:179711800-179714200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:179712000-179713000	Bivalent/Poised TSS	A549	lung
26	chr1:179712000-179713200	Bivalent Enhancer	Lung	lung
27	chr1:179712000-179713400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:179712000-179713400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
29	chr1:179712000-179713400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:179712000-179713600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:179712000-179713600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:179712000-179713600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:179712000-179713600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:179712000-179713800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:179712000-179713800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:179712000-179713800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
37	chr1:179712000-179714000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr1:179712000-179714000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:179712200-179712800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:179712200-179713000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr1:179712200-179713000	Flanking Active TSS	Gastric	stomach
42	chr1:179712200-179713000	Bivalent Enhancer	NHEK	skin
43	chr1:179712200-179713400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:179712200-179713400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:179712200-179713400	Flanking Active TSS	Pancreas	Pancrea
46	chr1:179712200-179713400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
47	chr1:179712200-179713600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:179712200-179713600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:179712200-179713600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:179712200-179713600	Bivalent/Poised TSS	HepG2	liver

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