Variant report

Variant	rs56028716
Chromosome Location	chr2:58399532-58399533
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10496087	0.80[AMR][1000 genomes]
rs12474593	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12475192	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12476829	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17049394	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049416	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17049417	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17049423	0.92[AMR][1000 genomes]
rs17326957	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36000054	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72810350	0.91[EUR][1000 genomes]
rs72810351	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72810352	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs72810363	0.84[EUR][1000 genomes]
rs72810385	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72810394	0.92[AMR][1000 genomes]
rs72812352	0.96[AMR][1000 genomes];0.88[EUR][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:63 , 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	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:58382600-58400400	Weak transcription	Gastric	stomach
9	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
12	chr2:58385200-58424600	Weak transcription	Ovary	ovary
13	chr2:58385400-58400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:58388800-58401800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:58389000-58423200	Weak transcription	NHLF	lung
17	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
18	chr2:58389800-58421000	Weak transcription	K562	blood
19	chr2:58390200-58421200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:58390400-58400800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:58391000-58467000	Weak transcription	HMEC	breast
22	chr2:58392200-58414200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:58392600-58408200	Weak transcription	A549	lung
24	chr2:58392600-58415600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:58393000-58404000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:58394000-58414800	Weak transcription	Hela-S3	cervix
27	chr2:58394600-58407800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:58394800-58405000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:58395600-58400400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:58396000-58399600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:58396400-58438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:58396400-58438000	Weak transcription	Pancreas	Pancrea
33	chr2:58396600-58399800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:58396800-58415200	Weak transcription	Dnd41	blood
35	chr2:58397200-58400400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:58397200-58400400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:58397400-58400400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:58397400-58400400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr2:58397800-58415200	Weak transcription	Liver	Liver
40	chr2:58397800-58442600	Weak transcription	Brain Anterior Caudate	brain
41	chr2:58398000-58400000	Weak transcription	Fetal Lung	lung
42	chr2:58398000-58415800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:58398000-58437800	Weak transcription	Primary B cells from cord blood	blood
44	chr2:58398600-58415600	Weak transcription	HepG2	liver
45	chr2:58398800-58399600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr2:58398800-58399600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr2:58398800-58399600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:58398800-58399600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:58398800-58399600	ZNF genes & repeats	Esophagus	oesophagus
50	chr2:58398800-58399600	ZNF genes & repeats	Spleen	Spleen

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