Variant report

Variant	rs848286
Chromosome Location	chr2:58394543-58394544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:58381634-58396003	K562	blood:	n/a	n/a
2	POLR2A	chr2:58394354-58394548	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FANCL	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10172212	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10188070	0.92[CEU][hapmap];0.82[GIH][hapmap]
rs1100190	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12477242	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs12620940	0.89[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2043890	0.89[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs3771221	0.83[EUR][1000 genomes]
rs3771224	0.82[EUR][1000 genomes]
rs6732310	0.84[MEX][hapmap]
rs72618694	0.82[EUR][1000 genomes]
rs72618695	0.82[EUR][1000 genomes]
rs72618696	0.84[EUR][1000 genomes]
rs7587962	0.80[YRI][hapmap]
rs848285	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs848287	0.92[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs848288	0.89[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs848289	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs848294	0.86[EUR][1000 genomes]
rs961522	0.82[GIH][hapmap]
rs986512	0.92[CEU][hapmap];0.84[JPT][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
rs848286	VRK2	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 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	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:58359200-58395200	Weak transcription	Fetal Stomach	stomach
5	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:58374400-58397400	Weak transcription	Fetal Heart	heart
13	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
14	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:58382600-58395400	Weak transcription	Pancreas	Pancrea
16	chr2:58382600-58395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
18	chr2:58382600-58400400	Weak transcription	Gastric	stomach
19	chr2:58382800-58395800	Weak transcription	Lung	lung
20	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:58383200-58398800	Weak transcription	Esophagus	oesophagus
25	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:58384200-58394800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:58384800-58395400	Weak transcription	Aorta	Aorta
28	chr2:58385000-58394600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
30	chr2:58385200-58398200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:58385200-58424600	Weak transcription	Ovary	ovary
32	chr2:58385400-58395600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:58385400-58400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:58387800-58396600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:58388200-58395600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:58388400-58395400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:58388400-58398200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:58388600-58397400	Weak transcription	Brain Anterior Caudate	brain
39	chr2:58388800-58397600	Weak transcription	Fetal Brain Female	brain
40	chr2:58388800-58401800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:58389000-58394600	Weak transcription	NHDF-Ad	bronchial
43	chr2:58389000-58395800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:58389000-58398000	Weak transcription	HSMM	muscle
45	chr2:58389000-58423200	Weak transcription	NHLF	lung
46	chr2:58389200-58394600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:58389200-58397600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:58389400-58397000	Weak transcription	Primary B cells from cord blood	blood
49	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
50	chr2:58389800-58395400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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