Variant report

Variant	rs13428078
Chromosome Location	chr2:58398102-58398103
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10167028	0.81[AFR][1000 genomes]
rs10179025	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10185542	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10185758	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10198382	0.84[AFR][1000 genomes]
rs10439485	1.00[AMR][1000 genomes]
rs13001078	0.84[AFR][1000 genomes]
rs13384786	0.84[AFR][1000 genomes]
rs13386998	0.84[AFR][1000 genomes]
rs13409706	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13417865	0.92[AFR][1000 genomes]
rs13418777	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13421853	0.89[AFR][1000 genomes]
rs13424099	0.86[AFR][1000 genomes]
rs13424848	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17182870	0.87[AFR][1000 genomes]
rs17183100	0.84[AFR][1000 genomes]
rs28391566	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28668929	0.84[AFR][1000 genomes]
rs3771214	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
12	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
14	chr2:58382600-58400400	Weak transcription	Gastric	stomach
15	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:58383200-58398800	Weak transcription	Esophagus	oesophagus
20	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
22	chr2:58385200-58398200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:58385200-58424600	Weak transcription	Ovary	ovary
24	chr2:58385400-58400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:58388400-58398200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:58388800-58401800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:58389000-58423200	Weak transcription	NHLF	lung
29	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
30	chr2:58389800-58421000	Weak transcription	K562	blood
31	chr2:58390000-58399000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:58390200-58421200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:58390400-58400800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:58390600-58398800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:58391000-58467000	Weak transcription	HMEC	breast
36	chr2:58392200-58398800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:58392200-58414200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:58392600-58408200	Weak transcription	A549	lung
39	chr2:58392600-58415600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:58393000-58404000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:58394000-58414800	Weak transcription	Hela-S3	cervix
42	chr2:58394600-58407800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:58394800-58405000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:58395600-58400400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:58396000-58399600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:58396400-58398800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:58396400-58398800	Weak transcription	Fetal Intestine Small	intestine
48	chr2:58396400-58398800	Weak transcription	Lung	lung
49	chr2:58396400-58399000	Weak transcription	Aorta	Aorta
50	chr2:58396400-58399000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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