Variant report

Variant	rs4820059
Chromosome Location	chr22:32346468-32346469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:32346267-32346819	GM12892	blood:	n/a	n/a
2	POLR2A	chr22:32346304-32346643	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:32346295-32346837	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr22:32346255-32347056	GM12892	blood:	n/a	n/a
5	POLR2A	chr22:32346286-32346748	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:32346190-32346597	K562	blood:	n/a	n/a
7	POLR2A	chr22:32346188-32346742	GM12891	blood:	n/a	n/a
8	POLR2A	chr22:32345555-32348344	K562	blood:	n/a	n/a
9	POLR2A	chr22:32346280-32346514	MCF-7	breast:	n/a	n/a
10	POLR2A	chr22:32346422-32346506	GM12878	blood:	n/a	n/a
11	POLR2A	chr22:32346385-32346672	HepG2	liver:	n/a	n/a
12	POLR2A	chr22:32346226-32346880	K562	blood:	n/a	n/a
13	POLR2A	chr22:32346461-32347241	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr22:32346261-32346750	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr22:32346257-32346959	GM12892	blood:	n/a	n/a
16	POLR2A	chr22:32346205-32348610	K562	blood:	n/a	n/a
17	POLR2A	chr22:32339799-32349498	K562	blood:	n/a	n/a
18	POLR2A	chr22:32346271-32347053	GM12892	blood:	n/a	n/a
19	POLR2A	chr22:32346291-32348270	A549	lung:	n/a	n/a
20	CTCF	chr22:32346320-32346470	HMF	breast:	n/a	n/a
21	POLR2A	chr22:32346419-32346515	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr22:32346360-32346510	HEK293	kidney:	n/a	n/a
23	POLR2A	chr22:32346261-32346816	GM12878	blood:	n/a	n/a
24	POLR2A	chr22:32346304-32346999	SK-N-MC	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32343477-32346868..22:32868055-32872511	K562	blood:
2	22:32053085-32061138..22:32343477-32346868	Hela-S3	cervix:
3	chr22:32329277..32332045-chr22:32345243..32347387,3	K562	blood:
4	chr22:32345809..32348159-chr22:32420362..32422364,2	MCF-7	breast:
5	chr22:32061496..32064184-chr22:32345416..32347899,2	K562	blood:
6	22:32170492-32188129..22:32343477-32346868	Hela-S3	cervix:
7	chr22:32269252..32272043-chr22:32344783..32347897,3	K562	blood:
8	chr22:32264603..32274220-chr22:32339477..32348693,21	K562	blood:
9	22:32264718-32278135..22:32343477-32346868	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238910	TF binding region
C22orf24	TF binding region
ENSG00000100150	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000241878	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1049583	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12168840	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs130262	0.81[CEU][hapmap]
rs13057194	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs135021	0.81[CEU][hapmap]
rs135023	0.81[CEU][hapmap]
rs135110	0.81[CEU][hapmap]
rs2246704	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2301415	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2853884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2853887	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2858750	0.87[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2858752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2858753	0.81[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs3747158	0.88[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4821004	0.81[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs5994457	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5994458	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5998196	0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs5998198	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7290696	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs7291050	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs7364274	0.87[ASW][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap]
rs738181	0.88[CHB][hapmap]
rs8141011	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs93108	0.81[CEU][hapmap]
rs933226	0.88[CHB][hapmap]
rs9609394	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9609395	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9609397	1.00[YRI][hapmap]
rs9621371	0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428046	chr22:32316302-32356963	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4820059	CHEK2	cis	cerebellum	SCAN
rs4820059	LARGE	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32342000-32347600	Weak transcription	Primary T cells from cord blood	blood
2	chr22:32342000-32354400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:32342200-32347200	Weak transcription	Ovary	ovary
4	chr22:32342200-32347600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr22:32342200-32347800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr22:32342400-32357600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr22:32342600-32346800	Weak transcription	Colonic Mucosa	Colon
8	chr22:32342800-32347800	Weak transcription	Psoas Muscle	Psoas
9	chr22:32343000-32346800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr22:32343200-32347600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr22:32343400-32347200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:32343400-32347200	Weak transcription	Small Intestine	intestine
13	chr22:32343400-32347400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr22:32343400-32347600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr22:32343400-32348000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr22:32343400-32348000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr22:32343400-32350400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr22:32343400-32355000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:32343600-32346600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr22:32343600-32346600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr22:32343600-32346600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr22:32343600-32346600	Weak transcription	Aorta	Aorta
23	chr22:32343600-32347000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr22:32343600-32347000	Strong transcription	Fetal Lung	lung
25	chr22:32343600-32347200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr22:32343600-32347400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr22:32343600-32347800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr22:32343600-32348800	Genic enhancers	K562	blood
29	chr22:32343600-32349200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr22:32343600-32349800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
31	chr22:32343600-32354600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr22:32343800-32346600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr22:32343800-32346600	Strong transcription	GM12878-XiMat	blood
34	chr22:32343800-32347200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr22:32343800-32347600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr22:32343800-32347800	Weak transcription	Liver	Liver
37	chr22:32343800-32351000	Strong transcription	Primary B cells from cord blood	blood
38	chr22:32344000-32346600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr22:32344000-32347000	Strong transcription	Fetal Intestine Small	intestine
40	chr22:32344000-32347200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr22:32344000-32347200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr22:32344000-32348200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr22:32344200-32347800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr22:32344200-32348000	Strong transcription	Fetal Intestine Large	intestine
45	chr22:32344200-32349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr22:32344400-32346800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr22:32344400-32347200	Strong transcription	Fetal Stomach	stomach
48	chr22:32344400-32348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr22:32344600-32346800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr22:32344600-32347200	Strong transcription	Dnd41	blood

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