Variant report

Variant	rs961522
Chromosome Location	chr2:58272502-58272503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr2:58272265-58273010	K562	blood:	n/a	n/a
2	POLR2A	chr2:58271722-58272616	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:58272024-58275047	GM18951	blood:	n/a	n/a
4	POLR2A	chr2:58271963-58275203	GM19193	blood:	n/a	n/a
5	POLR2A	chr2:58272318-58272607	GM12891	blood:	n/a	n/a
6	MAZ	chr2:58272442-58272519	K562	blood:	n/a	n/a
7	POLR2A	chr2:58272291-58272600	GM12892	blood:	n/a	n/a
8	POLR2A	chr2:58272171-58275631	GM18505	blood:	n/a	n/a
9	POLR2A	chr2:58272285-58272582	GM12892	blood:	n/a	n/a
10	CHD1	chr2:58271698-58275822	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:58271724-58272699	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:58271924-58272610	GM12892	blood:	n/a	n/a
13	POLR2A	chr2:58271253-58275620	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:58271753-58275667	GM12878	blood:	n/a	n/a
15	TBP	chr2:58272185-58273059	GM12878	blood:	n/a	n/a
16	WRNIP1	chr2:58271296-58272536	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr2:58272406-58272587	K562	blood:	n/a	n/a
18	POLR2A	chr2:58271686-58275020	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:58133863..58138456-chr2:58272095..58275151,4	MCF-7	breast:
2	chr2:58258901..58260862-chr2:58271685..58273683,2	K562	blood:
3	chr2:58272245..58275889-chr2:58464232..58469335,5	K562	blood:

No data

Variant related genes	Relation type
VRK2	TF binding region
ENSG00000115392	Chromatin interaction
ENSG00000273063	Chromatin interaction
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10188070	0.84[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10205421	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12620940	0.87[MEX][hapmap];0.80[TSI][hapmap]
rs12713370	0.81[EUR][1000 genomes]
rs1518395	0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs1518399	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2043890	0.87[MEX][hapmap];0.95[MKK][hapmap]
rs2312147	0.91[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2717027	0.80[EUR][1000 genomes]
rs6545677	0.84[EUR][1000 genomes]
rs6732310	0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs848286	0.82[GIH][hapmap]
rs848287	0.86[MEX][hapmap];0.83[MKK][hapmap]
rs848288	0.95[MKK][hapmap]
rs968653	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs986512	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][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	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs961522	VRK2	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58256800-58272800	Weak transcription	Adipose Nuclei	Adipose
2	chr2:58256800-58273000	Weak transcription	Pancreas	Pancrea
3	chr2:58258400-58273000	Weak transcription	Liver	Liver
4	chr2:58258800-58273000	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:58260000-58272800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:58260400-58273400	Weak transcription	Ovary	ovary
7	chr2:58262200-58273000	Weak transcription	Psoas Muscle	Psoas
8	chr2:58263000-58272800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:58266400-58272600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:58266600-58273000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:58266600-58273200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:58266800-58273400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:58268000-58273000	Weak transcription	Aorta	Aorta
14	chr2:58268000-58273200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:58268600-58273400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:58269200-58273000	Weak transcription	Esophagus	oesophagus
17	chr2:58269200-58273400	Weak transcription	Gastric	stomach
18	chr2:58270000-58272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:58270000-58272800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:58270000-58273000	Weak transcription	HSMM	muscle
21	chr2:58270000-58273400	Weak transcription	Fetal Brain Male	brain
22	chr2:58270200-58272600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:58270200-58272800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:58270200-58273200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:58270400-58272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:58270400-58272800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:58270400-58272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:58270400-58272800	Weak transcription	NHEK	skin
29	chr2:58270400-58272800	Weak transcription	Osteobl	bone
30	chr2:58270400-58273000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:58270400-58273200	Weak transcription	NH-A	brain
32	chr2:58271200-58272800	Enhancers	HUVEC	blood vessel
33	chr2:58271400-58272600	Flanking Active TSS	GM12878-XiMat	blood
34	chr2:58271400-58272800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:58271400-58273000	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:58271600-58272800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:58271600-58273200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:58271600-58273400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:58271800-58272600	Enhancers	HepG2	liver
40	chr2:58271800-58272800	Enhancers	Brain Hippocampus Middle	brain
41	chr2:58271800-58273000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr2:58271800-58273000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr2:58271800-58273200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr2:58271800-58273200	Enhancers	Primary hematopoietic stem cells	blood
45	chr2:58271800-58273200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:58271800-58273200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr2:58271800-58273400	Enhancers	Left Ventricle	heart
48	chr2:58272000-58272600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:58272000-58272600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr2:58272000-58272600	Enhancers	Small Intestine	intestine

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