Variant report

Variant	rs2716725
Chromosome Location	chr2:39952086-39952087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39941387..39944301-chr2:39949793..39952707,2	MCF-7	breast:
2	chr2:39949939..39952717-chr2:39956510..39959520,3	K562	blood:
3	chr2:39947562..39949942-chr2:39951658..39954303,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17024242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540231	1.00[AMR][1000 genomes]
rs2540232	1.00[AMR][1000 genomes]
rs2540237	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540238	0.89[AFR][1000 genomes]
rs2540239	0.89[AFR][1000 genomes]
rs2540240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540246	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716680	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716689	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716695	1.00[AMR][1000 genomes]
rs2716696	1.00[AMR][1000 genomes]
rs2716708	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716710	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716723	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716728	1.00[AMR][1000 genomes]
rs2716731	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57481251	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59943821	1.00[ASN][1000 genomes]
rs6746083	1.00[AMR][1000 genomes]
rs73924911	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924912	1.00[AMR][1000 genomes]
rs73924913	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924914	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924935	1.00[AMR][1000 genomes]
rs73924936	1.00[AMR][1000 genomes]
rs73924941	1.00[ASN][1000 genomes]
rs7559933	1.00[AMR][1000 genomes]
rs917968	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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
2	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:39938000-39957600	Weak transcription	Fetal Brain Female	brain
4	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:39943200-39956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
7	chr2:39945200-39954400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:39946800-39959600	Weak transcription	Brain Germinal Matrix	brain
9	chr2:39947800-39959800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:39948200-39961200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:39948800-39952400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39948800-39959600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:39949000-39952400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:39949000-39960400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:39949800-39952200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:39950000-39953400	Enhancers	NH-A	brain
17	chr2:39950000-39954400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:39950200-39952400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:39950600-39953000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:39950600-39953000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:39950600-39953200	Enhancers	HSMMtube	muscle
22	chr2:39950600-39953200	Enhancers	Osteobl	bone
23	chr2:39950800-39952200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:39950800-39952200	Enhancers	Fetal Kidney	kidney
25	chr2:39950800-39952400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:39950800-39952800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:39950800-39953600	Enhancers	HMEC	breast
28	chr2:39951000-39953400	Weak transcription	Left Ventricle	heart
29	chr2:39951000-39956000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:39951000-39957400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:39951000-39959400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:39951000-39963600	Weak transcription	Pancreas	Pancrea
33	chr2:39951000-39964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:39951200-39952200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:39951200-39952200	Enhancers	Fetal Heart	heart
36	chr2:39951200-39952400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:39951200-39952800	Enhancers	HSMM	muscle
38	chr2:39951200-39953200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:39951200-39957600	Weak transcription	Fetal Lung	lung
40	chr2:39951200-39964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:39951400-39957800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:39951400-39958800	Weak transcription	Aorta	Aorta
43	chr2:39951400-39960200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:39951400-39961400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:39951400-39961800	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:39951400-39962000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:39951400-39963800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:39951600-39953800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:39951800-39952400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:39951800-39953000	Bivalent Enhancer	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links