Variant report

Variant	rs72948870
Chromosome Location	chr2:58442613-58442614
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58442380..58445315-chr2:58458064..58460897,2	MCF-7	breast:
2	chr2:58442084..58444687-chr2:58485328..58487368,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs17049332	1.00[AMR][1000 genomes]
rs17049336	1.00[AMR][1000 genomes]
rs17049352	1.00[AMR][1000 genomes]
rs57334221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58150137	1.00[AMR][1000 genomes]
rs58276647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58321248	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58440082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58950743	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59323329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59350619	1.00[AMR][1000 genomes]
rs60949622	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60987670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6709203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732503	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6733307	1.00[AMR][1000 genomes]
rs72948807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948810	0.93[AFR][1000 genomes]
rs72948815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948859	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948895	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948898	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948900	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949121	1.00[AMR][1000 genomes]
rs72950804	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951053	1.00[AMR][1000 genomes]
rs72951061	1.00[AMR][1000 genomes]
rs72951063	1.00[AMR][1000 genomes]
rs72951079	1.00[AMR][1000 genomes]
rs72951080	1.00[AMR][1000 genomes]
rs72951097	1.00[AMR][1000 genomes]
rs72953110	1.00[AMR][1000 genomes]
rs72953112	1.00[AMR][1000 genomes]
rs72953119	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72953122	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72953124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72953130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579768	1.00[AMR][1000 genomes]
rs7580070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:58391000-58467000	Weak transcription	HMEC	breast
3	chr2:58414000-58461400	Weak transcription	NHEK	skin
4	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:58421600-58452400	Weak transcription	NH-A	brain
7	chr2:58422000-58442800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:58422000-58454200	Weak transcription	Left Ventricle	heart
9	chr2:58425600-58446600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:58425800-58446600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:58432000-58445600	Weak transcription	Osteobl	bone
12	chr2:58432000-58466400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:58433600-58454200	Weak transcription	Gastric	stomach
14	chr2:58437000-58460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:58437200-58442800	ZNF genes & repeats	GM12878-XiMat	blood
16	chr2:58437200-58459000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:58437600-58443200	Weak transcription	Right Atrium	heart
18	chr2:58437800-58456800	Weak transcription	Fetal Kidney	kidney
19	chr2:58438600-58443000	Weak transcription	Brain Germinal Matrix	brain
20	chr2:58438600-58443800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:58438600-58443800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:58438600-58444000	Strong transcription	A549	lung
23	chr2:58438600-58454200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:58438600-58454200	Weak transcription	Aorta	Aorta
25	chr2:58438600-58454200	Weak transcription	Esophagus	oesophagus
26	chr2:58438600-58454200	Weak transcription	Fetal Brain Female	brain
27	chr2:58438600-58454200	Weak transcription	Fetal Stomach	stomach
28	chr2:58438600-58454200	Weak transcription	Lung	lung
29	chr2:58438600-58454200	Weak transcription	Pancreas	Pancrea
30	chr2:58438600-58454200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:58438600-58454200	Weak transcription	Thymus	Thymus
32	chr2:58438600-58466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:58438800-58454200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:58438800-58454200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:58439000-58446600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:58439000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:58439200-58454200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:58439200-58454400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:58439200-58457000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:58439200-58457600	Weak transcription	Placenta	Placenta
41	chr2:58439400-58442800	Strong transcription	K562	blood
42	chr2:58439600-58443200	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:58439600-58454200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:58439800-58444200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:58439800-58445200	Weak transcription	Primary T cells from cord blood	blood
46	chr2:58439800-58449200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:58440000-58444200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:58440000-58445400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:58440000-58454200	Weak transcription	Primary B cells from cord blood	blood
50	chr2:58440000-58465000	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links