Variant report

Variant	rs2540237
Chromosome Location	chr2:39941390-39941391
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17024242	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540230	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540231	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540232	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540240	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540246	1.00[AMR][1000 genomes]
rs2716680	1.00[AMR][1000 genomes]
rs2716689	1.00[AMR][1000 genomes]
rs2716695	1.00[AMR][1000 genomes]
rs2716696	1.00[AMR][1000 genomes]
rs2716708	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716710	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716723	1.00[AMR][1000 genomes]
rs2716725	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716728	1.00[AMR][1000 genomes]
rs2716731	1.00[AMR][1000 genomes]
rs57481251	1.00[AMR][1000 genomes]
rs6746083	1.00[AMR][1000 genomes]
rs73924911	1.00[AMR][1000 genomes]
rs73924912	1.00[AMR][1000 genomes]
rs73924913	1.00[AMR][1000 genomes]
rs73924914	1.00[AMR][1000 genomes]
rs73924935	1.00[AMR][1000 genomes]
rs73924936	1.00[AMR][1000 genomes]
rs7559933	1.00[AMR][1000 genomes]
rs917968	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
2	chr2:39925200-39950000	Weak transcription	Left Ventricle	heart
3	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:39931600-39945800	Weak transcription	Aorta	Aorta
5	chr2:39934600-39941800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:39936600-39941600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:39936600-39950600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:39936800-39942200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:39937400-39948400	Weak transcription	Fetal Heart	heart
10	chr2:39938000-39941600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:39938000-39957600	Weak transcription	Fetal Brain Female	brain
12	chr2:39938200-39943200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:39938200-39950600	Weak transcription	HSMMtube	muscle
14	chr2:39938400-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:39938800-39947800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:39940400-39947000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:39940800-39950800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:39941200-39942800	Enhancers	Brain Hippocampus Middle	brain

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links