Variant report

Variant	rs17045084
Chromosome Location	chr2:53896048-53896049
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53887538..53889702-chr2:53894811..53897627,2	K562	blood:
2	chr2:53894424..53897447-chr2:53898122..53902216,4	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10490465	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11900355	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13428687	0.87[ASN][1000 genomes]
rs13428898	0.89[ASN][1000 genomes]
rs17039525	0.81[ASN][1000 genomes]
rs17045037	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17045048	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17045065	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17045081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34408637	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731970	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770407	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770408	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770409	0.92[ASN][1000 genomes]
rs3770411	0.84[AFR][1000 genomes]
rs3930	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4525731	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55861447	0.89[ASN][1000 genomes]
rs56081218	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56311225	0.88[ASN][1000 genomes]
rs56383522	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58125503	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58515086	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60282090	0.94[ASN][1000 genomes]
rs61671599	0.87[ASN][1000 genomes]
rs62139773	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62139774	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62139775	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62139785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62139788	0.94[ASN][1000 genomes]
rs62139836	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72901209	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73934971	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7600981	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:53881800-53896400	Weak transcription	Aorta	Aorta
4	chr2:53883200-53897800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:53883600-53896600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:53885800-53911800	Weak transcription	Adipose Nuclei	Adipose
8	chr2:53886600-53896400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:53887000-53898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:53887800-53899800	Weak transcription	Primary B cells from cord blood	blood
11	chr2:53888200-53934200	Weak transcription	Lung	lung
12	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
13	chr2:53888600-53897200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
15	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:53889400-53896800	Weak transcription	Fetal Lung	lung
17	chr2:53891600-53900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:53892600-53902600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:53892600-53918800	Weak transcription	Left Ventricle	heart
20	chr2:53893400-53915200	Weak transcription	Ovary	ovary
21	chr2:53893800-53926800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:53894200-53920800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:53894400-53900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:53894400-53912200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:53894400-53914400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:53894400-53925000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:53894600-53900000	Weak transcription	Stomach Mucosa	stomach
29	chr2:53894600-53911200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:53894800-53900000	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:53895000-53900200	Weak transcription	Brain Substantia Nigra	brain
32	chr2:53895000-53911800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr2:53895200-53898000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:53895400-53897000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:53895400-53898600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:53895400-53919000	Weak transcription	Fetal Intestine Large	intestine
37	chr2:53895400-53921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:53895400-53925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:53895400-53926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:53895600-53896200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:53895600-53897000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:53895600-53897400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:53895600-53914800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:53895600-53921400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:53895800-53896200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:53895800-53896200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr2:53895800-53896600	Enhancers	Fetal Heart	heart
48	chr2:53895800-53896800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:53895800-53897000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:53895800-53897000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links