Variant report

Variant	rs12620940
Chromosome Location	chr2:58311684-58311685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58272597..58275548-chr2:58309759..58311763,2	K562	blood:
2	chr2:58281941..58283918-chr2:58310687..58313540,2	K562	blood:
3	chr2:58310331..58313102-chr2:58313255..58316210,2	K562	blood:
4	chr2:58304898..58306855-chr2:58308067..58311851,3	K562	blood:
5	chr2:58286636..58288620-chr2:58310903..58313169,2	K562	blood:

Variant related genes	Relation type
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10172212	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10188070	0.89[CEU][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10205421	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10490251	0.81[JPT][hapmap]
rs1100190	0.86[AMR][1000 genomes]
rs12477242	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs12622856	0.94[JPT][hapmap]
rs12713370	0.82[JPT][hapmap]
rs1401100	0.84[MEX][hapmap]
rs1518395	0.82[JPT][hapmap];0.96[MEX][hapmap]
rs1518399	0.83[AMR][1000 genomes]
rs1568253	0.84[MEX][hapmap]
rs2043890	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]
rs2118899	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2139053	0.81[AMR][1000 genomes]
rs2312147	0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs2678880	0.84[MEX][hapmap]
rs2678889	0.84[MEX][hapmap]
rs2678908	1.00[LWK][hapmap];0.84[MEX][hapmap]
rs2717001	0.84[MEX][hapmap]
rs2717002	0.84[MEX][hapmap]
rs2717023	1.00[LWK][hapmap];0.87[MEX][hapmap]
rs2717024	1.00[LWK][hapmap];0.87[MEX][hapmap]
rs2717027	0.81[AMR][1000 genomes]
rs2717031	0.84[MEX][hapmap]
rs2717036	0.87[MEX][hapmap]
rs2717040	0.84[MEX][hapmap]
rs6545677	0.83[AMR][1000 genomes]
rs6732310	1.00[MEX][hapmap]
rs72618695	0.81[EUR][1000 genomes]
rs848285	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs848286	0.89[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs848287	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs848288	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]
rs848289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs848294	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs961522	0.87[MEX][hapmap];0.80[TSI][hapmap]
rs968653	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs986512	0.88[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription 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	26 gene(s)	inside rSNPs	diseases
4	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	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
6	nsv527551	chr2:58311684-58317208	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12620940	VRK2	cis	lymphoblastoid	seeQTL
rs12620940	VRK2	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58274800-58317400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:58275000-58317400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:58275000-58321600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
5	chr2:58275800-58316800	Weak transcription	HMEC	breast
6	chr2:58279000-58319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:58279400-58315600	Weak transcription	Dnd41	blood
8	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:58284200-58317600	Weak transcription	HepG2	liver
10	chr2:58284400-58325000	Weak transcription	NHEK	skin
11	chr2:58285200-58317000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:58286200-58317600	Weak transcription	K562	blood
13	chr2:58286400-58317600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:58287200-58315800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:58290400-58315800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:58291200-58316400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:58291600-58315600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:58291600-58316200	Weak transcription	HUVEC	blood vessel
19	chr2:58291600-58317800	Weak transcription	HSMM	muscle
20	chr2:58291600-58317800	Weak transcription	NH-A	brain
21	chr2:58291600-58319000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:58291600-58321800	Weak transcription	Fetal Thymus	thymus
23	chr2:58291600-58325000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:58291800-58318800	Weak transcription	Osteobl	bone
25	chr2:58292000-58316200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:58292200-58316200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:58292200-58319000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:58292200-58319000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:58294200-58320800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:58297000-58316800	Weak transcription	Ovary	ovary
31	chr2:58297600-58319000	Weak transcription	Primary T cells from cord blood	blood
32	chr2:58297800-58316400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:58297800-58317000	Weak transcription	Fetal Intestine Large	intestine
34	chr2:58298000-58315800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:58298000-58317600	Weak transcription	Left Ventricle	heart
36	chr2:58298200-58313400	Weak transcription	Liver	Liver
37	chr2:58298200-58315600	Weak transcription	Adipose Nuclei	Adipose
38	chr2:58298200-58316200	Weak transcription	Fetal Lung	lung
39	chr2:58298200-58317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:58301600-58319200	Weak transcription	Psoas Muscle	Psoas
41	chr2:58302400-58313400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:58302400-58315800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:58302400-58317200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:58302600-58312600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:58302600-58315200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:58302600-58315600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:58302600-58316200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:58302800-58314600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:58303000-58313600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:58303000-58315600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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