Variant report

Variant	rs62154558
Chromosome Location	chr2:98487414-98487415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs55804443	0.80[AFR][1000 genomes]
rs55853292	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55887737	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58415781	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58576615	0.89[AFR][1000 genomes]
rs58690282	0.80[AFR][1000 genomes]
rs59444417	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59635122	0.80[AFR][1000 genomes]
rs59752876	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60567628	0.84[AFR][1000 genomes]
rs61363543	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62154508	0.87[EUR][1000 genomes]
rs62154513	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62154516	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62154549	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154552	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62154553	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62154555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62154556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156480	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156482	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62156488	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62156507	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156508	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62156509	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62156519	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156522	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62156523	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62156524	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62156525	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62156526	0.80[AFR][1000 genomes]
rs62156527	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62156530	0.80[AFR][1000 genomes]
rs62157630	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73960406	0.84[AFR][1000 genomes]
rs73960426	0.84[AFR][1000 genomes]
rs73960430	0.82[AFR][1000 genomes]
rs73960433	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73960435	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7420897	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7575922	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7606272	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:98478600-98502200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:98478600-98502800	Weak transcription	Colonic Mucosa	Colon
4	chr2:98478600-98502800	Weak transcription	Pancreas	Pancrea
5	chr2:98478800-98489800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:98483800-98487600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:98484000-98487800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:98484000-98489200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:98485000-98487600	Enhancers	Duodenum Mucosa	Duodenum
10	chr2:98485000-98487800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:98485000-98487800	Enhancers	Fetal Heart	heart
12	chr2:98485000-98487800	Enhancers	Fetal Thymus	thymus
13	chr2:98485000-98487800	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:98485000-98488200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:98485000-98488200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:98485000-98488400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:98485000-98488400	Enhancers	Stomach Mucosa	stomach
18	chr2:98485200-98487600	Enhancers	Brain Hippocampus Middle	brain
19	chr2:98485200-98487800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:98485200-98487800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:98485200-98488000	Enhancers	HepG2	liver
22	chr2:98485200-98488200	Enhancers	Thymus	Thymus
23	chr2:98485200-98488400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:98485400-98488000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:98485600-98487600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:98485600-98488000	Enhancers	Brain Angular Gyrus	brain
27	chr2:98485600-98488400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:98485600-98488400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr2:98485600-98488600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:98485600-98488600	Enhancers	Placenta	Placenta
31	chr2:98485800-98487800	Enhancers	Primary B cells from cord blood	blood
32	chr2:98485800-98487800	Enhancers	Brain Substantia Nigra	brain
33	chr2:98485800-98488000	Enhancers	Liver	Liver
34	chr2:98485800-98488200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr2:98485800-98488400	Enhancers	Brain Anterior Caudate	brain
36	chr2:98486000-98488000	Enhancers	Primary T cells from cord blood	blood
37	chr2:98486000-98488200	Enhancers	Rectal Smooth Muscle	rectum
38	chr2:98486000-98488400	Enhancers	Ovary	ovary
39	chr2:98486000-98489200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr2:98486000-98489200	Enhancers	Colon Smooth Muscle	Colon
41	chr2:98486200-98487600	Weak transcription	Psoas Muscle	Psoas
42	chr2:98486200-98488200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:98486200-98488200	Enhancers	Fetal Lung	lung
44	chr2:98486200-98488400	Enhancers	NHEK	skin
45	chr2:98486200-98488600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr2:98486200-98489400	Weak transcription	Lung	lung
47	chr2:98486200-98490000	Weak transcription	Gastric	stomach
48	chr2:98486400-98488200	Enhancers	HUVEC	blood vessel
49	chr2:98486400-98488400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr2:98486400-98489000	Enhancers	Primary B cells from peripheral blood	blood

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