Variant report

Variant	rs848288
Chromosome Location	chr2:58392789-58392790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10172212	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10188070	0.89[CEU][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap]
rs10490251	0.94[JPT][hapmap];0.88[MKK][hapmap]
rs1100190	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12477242	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12620940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12622856	0.94[JPT][hapmap]
rs12713370	0.82[JPT][hapmap]
rs1518395	0.82[JPT][hapmap];0.87[MEX][hapmap]
rs2043890	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]
rs2118899	0.80[AMR][1000 genomes]
rs2312147	0.87[MEX][hapmap]
rs3771221	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771224	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6709203	0.89[YRI][hapmap]
rs6732310	0.91[MEX][hapmap]
rs72618694	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72618695	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72618696	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs848285	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs848286	0.89[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs848287	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848294	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs961522	0.95[MKK][hapmap]
rs986512	0.88[CEU][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs848288	VRK2	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 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	chr2:58358200-58393800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:58359200-58395200	Weak transcription	Fetal Stomach	stomach
6	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:58374400-58393400	Weak transcription	NHEK	skin
14	chr2:58374400-58397400	Weak transcription	Fetal Heart	heart
15	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
16	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:58382200-58393200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:58382600-58394000	Weak transcription	Fetal Brain Male	brain
19	chr2:58382600-58395400	Weak transcription	Pancreas	Pancrea
20	chr2:58382600-58395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
22	chr2:58382600-58400400	Weak transcription	Gastric	stomach
23	chr2:58382800-58394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:58382800-58395800	Weak transcription	Lung	lung
25	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:58383200-58398800	Weak transcription	Esophagus	oesophagus
30	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:58384000-58393800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:58384200-58394800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:58384600-58393000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:58384600-58393000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:58384600-58393000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:58384800-58395400	Weak transcription	Aorta	Aorta
37	chr2:58385000-58394600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
39	chr2:58385200-58398200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:58385200-58424600	Weak transcription	Ovary	ovary
41	chr2:58385400-58395600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:58385400-58400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:58387800-58396600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:58388200-58395600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:58388400-58395400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:58388400-58398200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:58388600-58394400	Weak transcription	NH-A	brain
48	chr2:58388600-58397400	Weak transcription	Brain Anterior Caudate	brain
49	chr2:58388800-58394200	Weak transcription	GM12878-XiMat	blood
50	chr2:58388800-58397600	Weak transcription	Fetal Brain Female	brain

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