Variant report

Variant	rs12125349
Chromosome Location	chr1:184506303-184506304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184498410..184500025-chr1:184504648..184506680,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1007224	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10737253	0.80[ASN][1000 genomes]
rs10797971	0.87[ASN][1000 genomes]
rs10797972	0.91[ASN][1000 genomes]
rs10797977	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10911606	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11588922	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12127674	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339563	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1339564	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1339565	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339566	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1339567	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1569842	0.80[ASN][1000 genomes]
rs1884200	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2001270	0.94[ASN][1000 genomes]
rs2038307	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2038308	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2144294	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2180073	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2180077	0.80[ASN][1000 genomes]
rs2207528	0.80[ASN][1000 genomes]
rs2378888	0.95[ASN][1000 genomes]
rs2890014	0.80[EUR][1000 genomes]
rs2890015	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4650667	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4651208	0.80[ASN][1000 genomes]
rs4651210	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651211	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4651216	0.91[ASN][1000 genomes]
rs4651217	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651218	0.80[EUR][1000 genomes]
rs4651219	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55729410	0.80[ASN][1000 genomes]
rs6666704	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7517518	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7533466	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544240	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970984	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970990	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184501800-184510200	Weak transcription	NHEK	skin
2	chr1:184502400-184517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:184502400-184520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:184502600-184527200	Weak transcription	Fetal Brain Female	brain
5	chr1:184503200-184514600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:184503200-184516400	Weak transcription	Fetal Brain Male	brain
7	chr1:184503400-184515800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:184503400-184520400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:184504000-184507000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:184504000-184507200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:184504200-184508600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:184504200-184522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:184504400-184508200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr1:184504400-184508800	Weak transcription	Psoas Muscle	Psoas
15	chr1:184504400-184510600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:184504800-184507000	Weak transcription	Fetal Heart	heart
17	chr1:184504800-184508000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:184505400-184506800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:184505400-184507800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:184505400-184509200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:184505400-184511400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:184505600-184507800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:184505600-184508800	Weak transcription	Ovary	ovary
24	chr1:184505600-184511600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:184505600-184511800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:184505800-184508800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:184505800-184510600	Weak transcription	Right Atrium	heart
28	chr1:184505800-184510800	Weak transcription	Fetal Intestine Large	intestine
29	chr1:184505800-184511200	Weak transcription	Left Ventricle	heart
30	chr1:184505800-184511200	Weak transcription	Right Ventricle	heart
31	chr1:184505800-184511400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:184505800-184511400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:184505800-184513000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:184505800-184514600	Weak transcription	NHLF	lung
35	chr1:184505800-184515000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:184505800-184515800	Weak transcription	Lung	lung
37	chr1:184505800-184516000	Weak transcription	Pancreas	Pancrea
38	chr1:184505800-184518200	Weak transcription	Gastric	stomach
39	chr1:184505800-184524000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:184505800-184530800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:184505800-184531600	Weak transcription	Fetal Stomach	stomach
42	chr1:184506000-184507600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:184506000-184508600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:184506200-184520600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links