Variant report

Variant	rs4459722
Chromosome Location	chr2:58269206-58269207
allele	C/T
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	TCF12	chr2:58269151-58270331	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr2:58269084-58270284	SK-N-SH	brain:	n/a	chr2:58269961-58269970 chr2:58269631-58269641 chr2:58269632-58269639 chr2:58269630-58269642
3	EP300	chr2:58269146-58270210	SK-N-SH	brain:	n/a	chr2:58269759-58269773 chr2:58269960-58269969 chr2:58269993-58270007 chr2:58269757-58269771
4	IRF1	chr2:58269059-58269219	K562	blood:	n/a	n/a
5	PBX3	chr2:58268998-58270259	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr2:58269115-58270229	SK-N-SH	brain:	n/a	chr2:58269839-58269855 chr2:58269838-58269855 chr2:58269837-58269854
7	TCF12	chr2:58269147-58270292	SK-N-SH	brain:	n/a	n/a
8	GATA2	chr2:58269164-58269983	HUVEC	blood vessel:	n/a	chr2:58269961-58269970 chr2:58269631-58269641 chr2:58269632-58269639 chr2:58269630-58269642
9	GATA3	chr2:58269065-58270250	SK-N-SH	brain:	n/a	chr2:58269961-58269970 chr2:58269631-58269641 chr2:58269632-58269639 chr2:58269630-58269642

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58268085..58271557-chr2:58272019..58276950,11	MCF-7	breast:
2	chr2:58268209..58270134-chr2:58271318..58274242,3	K562	blood:

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

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10164499	0.85[AMR][1000 genomes]
rs10165760	0.89[AFR][1000 genomes]
rs10174202	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10176681	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10178025	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10182762	0.86[AFR][1000 genomes]
rs10187411	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10191766	0.87[AMR][1000 genomes]
rs10201793	0.87[AMR][1000 genomes]
rs10203014	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1025755	0.87[AFR][1000 genomes]
rs10518852	0.87[AMR][1000 genomes]
rs11883874	0.89[AFR][1000 genomes]
rs11891477	0.86[AFR][1000 genomes]
rs11892302	0.87[AFR][1000 genomes]
rs13382369	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13394820	0.92[AFR][1000 genomes]
rs13400997	0.87[AMR][1000 genomes]
rs13405281	0.89[AFR][1000 genomes]
rs13410500	0.89[AFR][1000 genomes]
rs13419989	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13431271	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2165100	0.89[AFR][1000 genomes]
rs2165103	0.87[AFR][1000 genomes]
rs28521626	0.92[AFR][1000 genomes]
rs57597086	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58470176	0.89[AFR][1000 genomes]
rs6718190	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949131	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949137	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949158	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951042	0.85[AFR][1000 genomes]
rs72951048	0.89[AFR][1000 genomes]
rs72951056	0.89[AFR][1000 genomes]
rs73944804	0.86[AFR][1000 genomes]
rs7563225	0.87[AMR][1000 genomes]
rs7563312	0.83[AFR][1000 genomes]
rs7569731	0.84[AFR][1000 genomes]
rs7574578	0.87[AMR][1000 genomes]
rs7574694	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7600213	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9973345	0.81[AFR][1000 genomes]
rs9973928	0.87[AFR][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	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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58251400-58272000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:58256600-58271800	Weak transcription	Left Ventricle	heart
3	chr2:58256800-58272800	Weak transcription	Adipose Nuclei	Adipose
4	chr2:58256800-58273000	Weak transcription	Pancreas	Pancrea
5	chr2:58258200-58271800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:58258400-58273000	Weak transcription	Liver	Liver
7	chr2:58258600-58272000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:58258800-58273000	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:58259400-58269400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:58260000-58272800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:58260200-58271800	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:58260400-58273400	Weak transcription	Ovary	ovary
13	chr2:58262200-58273000	Weak transcription	Psoas Muscle	Psoas
14	chr2:58263000-58272800	Weak transcription	Brain Anterior Caudate	brain
15	chr2:58266400-58272600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:58266600-58269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:58266600-58269600	Weak transcription	NHLF	lung
18	chr2:58266600-58271800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:58266600-58271800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:58266600-58272000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:58266600-58272400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:58266600-58273000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:58266600-58273200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:58266800-58269400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:58266800-58269600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:58266800-58269600	Weak transcription	Osteobl	bone
27	chr2:58266800-58270800	Enhancers	HUVEC	blood vessel
28	chr2:58266800-58271800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:58266800-58272000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:58266800-58272000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:58266800-58273400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:58267000-58269400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:58267000-58269400	Weak transcription	NHDF-Ad	bronchial
34	chr2:58267000-58272400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr2:58267200-58271400	Weak transcription	Primary B cells from cord blood	blood
36	chr2:58267200-58271400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr2:58267200-58272400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:58267400-58269600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:58267400-58269600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:58267800-58269400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:58267800-58269600	Enhancers	A549	lung
42	chr2:58268000-58269600	Weak transcription	K562	blood
43	chr2:58268000-58270400	Enhancers	NHEK	skin
44	chr2:58268000-58272200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:58268000-58273000	Weak transcription	Aorta	Aorta
46	chr2:58268000-58273200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:58268200-58269600	Weak transcription	GM12878-XiMat	blood
48	chr2:58268200-58270400	Enhancers	HepG2	liver
49	chr2:58268200-58272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:58268400-58269400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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