Variant report

Variant	rs28496426
Chromosome Location	chr2:54746773-54746774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10169013	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171393	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172671	1.00[ASN][1000 genomes]
rs10182310	1.00[ASN][1000 genomes]
rs10188548	1.00[ASN][1000 genomes]
rs10189084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189455	0.83[EUR][1000 genomes]
rs10191357	1.00[ASN][1000 genomes]
rs10194488	1.00[ASN][1000 genomes]
rs10195423	1.00[ASN][1000 genomes]
rs10206622	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388685	0.83[EUR][1000 genomes]
rs13391762	1.00[ASN][1000 genomes]
rs13403817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414727	1.00[ASN][1000 genomes]
rs13415413	1.00[ASN][1000 genomes]
rs13415949	1.00[ASN][1000 genomes]
rs13418525	0.83[EUR][1000 genomes]
rs13423872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425620	1.00[ASN][1000 genomes]
rs13426037	1.00[ASN][1000 genomes]
rs13427468	1.00[ASN][1000 genomes]
rs13428524	1.00[ASN][1000 genomes]
rs13431302	1.00[ASN][1000 genomes]
rs13431815	0.83[EUR][1000 genomes]
rs17045949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229505	1.00[ASN][1000 genomes]
rs28609649	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660202	1.00[ASN][1000 genomes]
rs28679552	1.00[ASN][1000 genomes]
rs4387841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545404	0.83[EUR][1000 genomes]
rs6545417	1.00[ASN][1000 genomes]
rs6545426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723740	0.83[EUR][1000 genomes]
rs6735962	1.00[ASN][1000 genomes]
rs6743995	0.83[EUR][1000 genomes]
rs6746379	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757240	0.83[EUR][1000 genomes]
rs7340250	1.00[ASN][1000 genomes]
rs7355672	0.83[EUR][1000 genomes]
rs73934326	1.00[ASN][1000 genomes]
rs7574433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808516	1.00[ASN][1000 genomes]
rs9967676	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:54733600-54747000	Weak transcription	Gastric	stomach
5	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
6	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
7	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
8	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:54740400-54747000	Weak transcription	Pancreas	Pancrea
11	chr2:54740400-54747800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:54740400-54751600	Weak transcription	Placenta	Placenta
13	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
14	chr2:54740600-54746800	Weak transcription	Osteobl	bone
15	chr2:54740600-54747000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:54740600-54749800	Weak transcription	HepG2	liver
17	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:54740800-54746800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:54740800-54747000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:54741000-54748000	Weak transcription	Adipose Nuclei	Adipose
22	chr2:54742000-54747000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:54742400-54747400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:54742400-54748000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:54742600-54746800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:54742600-54747800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:54742800-54750600	Weak transcription	Brain Germinal Matrix	brain
28	chr2:54743400-54748200	Enhancers	Fetal Heart	heart
29	chr2:54743600-54751600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:54744000-54747200	Weak transcription	HSMMtube	muscle
31	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:54744200-54747000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:54744400-54748000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:54744400-54751400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:54744400-54753400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:54744400-54753400	Weak transcription	Ovary	ovary
37	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
38	chr2:54744600-54748000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:54744600-54753400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:54745000-54748000	Weak transcription	Lung	lung
41	chr2:54745200-54746800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:54745200-54747400	Enhancers	Brain Hippocampus Middle	brain
43	chr2:54745600-54748600	Enhancers	HMEC	breast
44	chr2:54745800-54747000	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr2:54745800-54747400	Enhancers	Brain Angular Gyrus	brain
46	chr2:54746000-54747000	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:54746000-54747600	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr2:54746000-54748600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:54746200-54746800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr2:54746200-54747200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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