Variant report

Variant	rs59264390
Chromosome Location	chr2:58272110-58272111
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	PBX3	chr2:58272029-58272296	GM12878	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	chr2:58271957-58272242	GM12891	blood:	n/a	n/a
6	CHD1	chr2:58271698-58275822	GM12878	blood:	n/a	n/a
7	EBF1	chr2:58272005-58272318	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:58271724-58272699	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:58271924-58272610	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:58271253-58275620	GM12891	blood:	n/a	n/a
11	POLR2A	chr2:58271753-58275667	GM12878	blood:	n/a	n/a
12	WRNIP1	chr2:58271296-58272536	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:58271686-58275020	GM12878	blood:	n/a	n/a

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	chr2:58269958..58272240-chr2:58464322..58467065,2	K562	blood:

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

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17049347	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049370	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049374	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049404	1.00[AMR][1000 genomes]
rs55925609	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56878245	1.00[AMR][1000 genomes]
rs58495080	1.00[AMR][1000 genomes]
rs58984910	0.87[AFR][1000 genomes]
rs59299963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59871174	1.00[AMR][1000 genomes]
rs60912631	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61126591	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61415878	1.00[AMR][1000 genomes]
rs6741122	1.00[AMR][1000 genomes]
rs73942251	1.00[AMR][1000 genomes]
rs73942258	1.00[AMR][1000 genomes]
rs73942281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944812	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944819	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944823	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944825	0.82[AFR][1000 genomes]
rs73944826	1.00[AMR][1000 genomes]
rs73944827	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944828	1.00[AMR][1000 genomes]
rs73944835	1.00[AMR][1000 genomes]
rs73944837	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944838	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944839	1.00[AMR][1000 genomes]
rs73944840	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7587116	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7587229	0.96[AFR][1000 genomes];1.00[AMR][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

No data

Chromatin state (count:87 , 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	chr2:58266600-58272400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:58266600-58273000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:58266600-58273200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:58266800-58273400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:58267000-58272400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:58267200-58272400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:58268000-58272200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:58268000-58273000	Weak transcription	Aorta	Aorta
18	chr2:58268000-58273200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:58268600-58273400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:58269200-58273000	Weak transcription	Esophagus	oesophagus
21	chr2:58269200-58273400	Weak transcription	Gastric	stomach
22	chr2:58270000-58272400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:58270000-58272400	Weak transcription	NHLF	lung
24	chr2:58270000-58272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:58270000-58272800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:58270000-58273000	Weak transcription	HSMM	muscle
27	chr2:58270000-58273400	Weak transcription	Fetal Brain Male	brain
28	chr2:58270200-58272200	Weak transcription	Fetal Heart	heart
29	chr2:58270200-58272200	Weak transcription	NHDF-Ad	bronchial
30	chr2:58270200-58272400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:58270200-58272400	Weak transcription	HMEC	breast
32	chr2:58270200-58272600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:58270200-58272800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:58270200-58273200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:58270400-58272400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:58270400-58272400	Weak transcription	Hela-S3	cervix
37	chr2:58270400-58272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:58270400-58272800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:58270400-58272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:58270400-58272800	Weak transcription	NHEK	skin
41	chr2:58270400-58272800	Weak transcription	Osteobl	bone
42	chr2:58270400-58273000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:58270400-58273200	Weak transcription	NH-A	brain
44	chr2:58271200-58272200	Genic enhancers	A549	lung
45	chr2:58271200-58272800	Enhancers	HUVEC	blood vessel
46	chr2:58271400-58272200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:58271400-58272200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:58271400-58272200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:58271400-58272600	Flanking Active TSS	GM12878-XiMat	blood
50	chr2:58271400-58272800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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