Variant report

Variant	rs2043890
Chromosome Location	chr2:58350571-58350572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58350031..58352621-chr2:58354881..58357674,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10172212	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10188070	0.89[CEU][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10205421	0.82[EUR][1000 genomes]
rs10490251	1.00[ASW][hapmap];0.87[JPT][hapmap];0.88[MKK][hapmap]
rs1100190	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12477242	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12620940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622856	1.00[JPT][hapmap]
rs12713370	0.88[JPT][hapmap]
rs1401100	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs1518395	0.88[JPT][hapmap];0.96[MEX][hapmap]
rs1518399	0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs1568252	0.83[JPT][hapmap]
rs1568253	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs2118899	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2312147	0.83[JPT][hapmap];0.96[MEX][hapmap]
rs2678870	0.83[JPT][hapmap]
rs2678880	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs2678889	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs2678897	0.83[JPT][hapmap]
rs2717019	0.83[JPT][hapmap]
rs2717023	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs2717024	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs2717031	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs2717036	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs2717040	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs2717043	0.83[JPT][hapmap]
rs3771221	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3771224	0.84[EUR][1000 genomes]
rs6545677	0.83[JPT][hapmap]
rs6732310	0.83[JPT][hapmap];1.00[MEX][hapmap]
rs72618694	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72618695	0.85[EUR][1000 genomes]
rs72618696	0.82[EUR][1000 genomes]
rs848285	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs848286	0.89[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs848287	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs848288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs848289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs848294	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs961522	0.87[MEX][hapmap];0.95[MKK][hapmap]
rs968653	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs970941	0.83[JPT][hapmap]
rs986512	0.88[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2043890	VRK2	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58303000-58358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
3	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:58319400-58358400	Weak transcription	Ovary	ovary
6	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:58320000-58359000	Weak transcription	Left Ventricle	heart
10	chr2:58332400-58370800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:58335800-58350600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:58335800-58358600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:58336400-58365000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:58337000-58358600	Weak transcription	NHLF	lung
15	chr2:58337200-58358400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:58338000-58358400	Weak transcription	Fetal Stomach	stomach
17	chr2:58338200-58365400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:58338800-58359000	Weak transcription	HepG2	liver
19	chr2:58340000-58358400	Weak transcription	NH-A	brain
20	chr2:58340600-58358400	Weak transcription	HMEC	breast
21	chr2:58340600-58363000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:58340600-58367000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:58340600-58373600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:58344400-58386000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:58346000-58358600	Weak transcription	Fetal Lung	lung
26	chr2:58346000-58384400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:58346600-58358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:58346600-58373600	Weak transcription	NHEK	skin
29	chr2:58346800-58387200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:58347000-58360800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:58347200-58360200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:58347200-58373800	Weak transcription	Hela-S3	cervix
33	chr2:58347600-58352600	Strong transcription	Primary B cells from cord blood	blood
34	chr2:58347800-58369800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:58347800-58384000	Weak transcription	Fetal Kidney	kidney
36	chr2:58347800-58386600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:58348000-58360600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:58348200-58350600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:58348200-58358600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:58348200-58360600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:58348400-58358400	Weak transcription	NHDF-Ad	bronchial
42	chr2:58348400-58373400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:58348400-58373600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:58348600-58382400	Weak transcription	Fetal Intestine Large	intestine
45	chr2:58348800-58357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:58348800-58365600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:58349000-58351600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:58349000-58358400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:58349000-58358400	Weak transcription	Pancreas	Pancrea
50	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain

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