Variant report

Variant	rs55809167
Chromosome Location	chr2:58407947-58407948
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10184957	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11903212	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12616896	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12624152	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713376	0.97[EUR][1000 genomes]
rs12988249	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13006005	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13023405	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032851	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13410228	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13422760	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1404457	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1404459	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1404460	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34335951	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34556232	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35773188	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35925771	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755296	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771222	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57267169	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61746304	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6709533	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6714952	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6752935	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558066	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7561771	0.90[EUR][1000 genomes];0.90[ASN][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:54 , 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	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
8	chr2:58385200-58424600	Weak transcription	Ovary	ovary
9	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:58389000-58423200	Weak transcription	NHLF	lung
11	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
12	chr2:58389800-58421000	Weak transcription	K562	blood
13	chr2:58390200-58421200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:58391000-58467000	Weak transcription	HMEC	breast
15	chr2:58392200-58414200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:58392600-58408200	Weak transcription	A549	lung
17	chr2:58392600-58415600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:58394000-58414800	Weak transcription	Hela-S3	cervix
19	chr2:58396400-58438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:58396400-58438000	Weak transcription	Pancreas	Pancrea
21	chr2:58396800-58415200	Weak transcription	Dnd41	blood
22	chr2:58397800-58415200	Weak transcription	Liver	Liver
23	chr2:58397800-58442600	Weak transcription	Brain Anterior Caudate	brain
24	chr2:58398000-58415800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:58398000-58437800	Weak transcription	Primary B cells from cord blood	blood
26	chr2:58398600-58415600	Weak transcription	HepG2	liver
27	chr2:58399400-58413400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:58399400-58414600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:58399400-58437400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:58399600-58413200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:58399800-58421800	Weak transcription	Fetal Stomach	stomach
32	chr2:58399800-58426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:58400200-58409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:58400400-58408200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:58400400-58409800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:58400400-58413400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:58400400-58413600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:58400400-58415400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:58400400-58437800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:58401600-58410000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:58401600-58415600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:58403000-58439400	Weak transcription	HSMM	muscle
43	chr2:58403600-58434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:58403600-58437200	Weak transcription	Fetal Brain Female	brain
45	chr2:58405600-58415200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:58405600-58415400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:58407200-58408600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:58407400-58415400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:58407400-58424000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:58407600-58408000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links