Variant report

Variant	rs4821004
Chromosome Location	chr22:32366359-32366360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:215)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:215 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr22:32365967-32367117	HCT-116	colon:	n/a	chr22:32366769-32366782 chr22:32366338-32366352
2	CTCF	chr22:32365987-32366431	GM12892	blood:	n/a	n/a
3	CTCF	chr22:32366016-32366457	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZEB1	chr22:32365854-32367012	GM12878	blood:	n/a	n/a
5	CTCF	chr22:32366155-32366383	Lung_OC	lung:	n/a	n/a
6	CTCF	chr22:32366240-32366390	HFF-Myc	foreskin:	n/a	n/a
7	CTCF	chr22:32366053-32366403	GM19239	blood:	n/a	n/a
8	RAD21	chr22:32365795-32367134	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr22:32366029-32366404	GM12878	blood:	n/a	n/a
10	CTCF	chr22:32366220-32366370	AG04449	skin:	n/a	n/a
11	CTCF	chr22:32366220-32366370	HEK293	kidney:	n/a	n/a
12	MAX	chr22:32366007-32367130	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr22:32366220-32366370	HCM	heart:	n/a	n/a
14	CTCF	chr22:32366260-32366410	NB4	blood:	n/a	n/a
15	CTCF	chr22:32366079-32367040	K562	blood:	n/a	n/a
16	RAD21	chr22:32365865-32367086	H1-hESC	embryonic stem cell:	n/a	n/a
17	UBTF	chr22:32366261-32366456	K562	blood:	n/a	n/a
18	EGR1	chr22:32366149-32366444	K562	blood:	n/a	chr22:32366338-32366352
19	RFX5	chr22:32366301-32366423	HepG2	liver:	n/a	chr22:32366353-32366368
20	USF1	chr22:32366102-32366501	K562	blood:	n/a	n/a
21	RAD21	chr22:32365969-32366523	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr22:32366137-32366389	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr22:32365826-32367227	SK-N-SH	brain:	n/a	n/a
24	MAZ	chr22:32366237-32366413	HepG2	liver:	n/a	n/a
25	CTCF	chr22:32366177-32366396	GM10248	blood:	n/a	n/a
26	CTCF	chr22:32366260-32366410	HFF	foreskin:	n/a	n/a
27	YY1	chr22:32366022-32366376	GM12892	blood:	n/a	n/a
28	CTCF	chr22:32366029-32366429	K562	blood:	n/a	n/a
29	RAD21	chr22:32365960-32366423	K562	blood:	n/a	n/a
30	RAD21	chr22:32366047-32366391	GM12878	blood:	n/a	n/a
31	RCOR1	chr22:32366122-32366427	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr22:32366099-32367092	H1-neurons	neurons:	n/a	n/a
33	MAX	chr22:32366067-32366493	SK-N-SH	brain:	n/a	n/a
34	RCOR1	chr22:32366079-32367123	K562	blood:	n/a	n/a
35	CTCF	chr22:32366220-32366370	HUVEC	blood vessel:	n/a	n/a
36	MYC	chr22:32366108-32366973	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr22:32366114-32366428	GM19240	blood:	n/a	n/a
38	MAFK	chr22:32366166-32366428	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr22:32366046-32366448	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr22:32366141-32366410	H1-hESC	embryonic stem cell:	n/a	n/a
41	TCF12	chr22:32366050-32366449	H1-hESC	embryonic stem cell:	n/a	n/a
42	BACH1	chr22:32366154-32367033	H1-hESC	embryonic stem cell:	n/a	n/a
43	TAF1	chr22:32366164-32367087	H1-neurons	neurons:	n/a	n/a
44	JUND	chr22:32366114-32367437	K562	blood:	n/a	n/a
45	CTCF	chr22:32365942-32367199	MCF-7	breast:	n/a	n/a
46	MYC	chr22:32366119-32366885	MCF10A-Er-Src	breast:	n/a	n/a
47	CTCF	chr22:32366139-32366401	MCF-7	breast:	n/a	n/a
48	CTCF	chr22:32365973-32366449	K562	blood:	n/a	n/a
49	USF1	chr22:32366186-32366554	ECC-1	luminal epithelium:	n/a	n/a
50	ZEB1	chr22:32365957-32367088	HepG2	liver:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62609146..62610653-chr22:32365275..32366775,2	K562	blood:
2	chr22:32365255..32366775-chr3:73159952..73161574,3	K562	blood:
3	chr11:62609150..62609700-chr22:32366255..32366775,2	MCF-7	breast:
4	chr17:41464701..41467719-chr22:32365255..32368255,4	MCF-7	breast:
5	chr11:62609149..62609721-chr22:32366275..32366775,2	HCT-116	colon:
6	22:32360288-32405313..22:32764253-32784733	K562	blood:
7	chr22:31952335..31953173-chr22:32365824..32366681,2	MCF-7	breast:
8	chr22:32365255..32368255-chr3:73159964..73161574,3	K562	blood:
9	22:32360288-32405313..22:32868055-32872511	K562	blood:
10	22:32012966-32043914..22:32360288-32405313	K562	blood:
11	chr22:32340998..32345394-chr22:32364660..32368897,5	MCF-7	breast:
12	22:32360288-32405313..22:33452523-33459358	H1-hESC	embryonic stem cell:	embryo
13	chr22:32061316..32062330-chr22:32365767..32366693,3	K562	blood:
14	22:32360288-32405313..22:32750950-32761732	K562	blood:
15	22:32360288-32405313..22:32860159-32865649	K562	blood:
16	22:32360288-32405313..22:32740683-32750950	K562	blood:
17	chr22:32268348..32268930-chr22:32365701..32366478,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YWHAH-1	chr22:32365973-32366387	XLOC_014211
2	lnc-YWHAH-1	chr22:32365849-32366387	NONHSAT084924

No data

Variant related genes	Relation type
ENSG00000230866	TF binding region
ENSG00000243519	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000128245	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000241954	Chromatin interaction
ENSG00000205853	Chromatin interaction
ENSG00000230736	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000232218	Chromatin interaction
ENSG00000271093	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000128254	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1056444	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs12484973	0.81[JPT][hapmap]
rs130260	0.85[EUR][1000 genomes]
rs130261	0.84[EUR][1000 genomes]
rs130262	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs130266	0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs130407	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs13055495	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13057194	0.81[EUR][1000 genomes]
rs135020	0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs135021	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs135023	1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs135110	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs135111	0.81[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs1807550	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1986211	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246704	0.92[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2301415	0.83[MEX][hapmap]
rs2413061	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2858750	0.83[MEX][hapmap]
rs2858753	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3747158	0.84[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs4820059	0.81[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4820065	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4821014	0.82[YRI][hapmap]
rs5753843	0.82[YRI][hapmap]
rs5753852	0.90[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs5994457	0.84[EUR][1000 genomes]
rs5994458	0.82[EUR][1000 genomes]
rs5994461	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5994466	0.82[GIH][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap]
rs5998196	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5998198	0.86[EUR][1000 genomes]
rs5998201	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5998204	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5998233	0.81[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap]
rs5998237	0.81[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs739009	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs8137665	0.81[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs8141011	0.83[MEX][hapmap]
rs8142505	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs93108	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs9606906	0.81[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]

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	nsv1055450	chr22:32356150-32468832	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1055925	chr22:32358540-32450200	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1063876	chr22:32358540-32463271	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1061546	chr22:32358991-32464350	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1059240	chr22:32362689-32462511	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv544678	chr22:32362689-32462511	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4821004	CHEK2	cis	cerebellum	SCAN
rs4821004	LARGE	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32351400-32366400	Weak transcription	Right Atrium	heart
2	chr22:32353400-32366400	Weak transcription	Psoas Muscle	Psoas
3	chr22:32354400-32366400	Weak transcription	Colonic Mucosa	Colon
4	chr22:32354600-32366400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr22:32354600-32366400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr22:32354600-32366400	Weak transcription	NHLF	lung
7	chr22:32354800-32366400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr22:32354800-32366400	Weak transcription	HSMM	muscle
9	chr22:32355000-32366400	Weak transcription	Left Ventricle	heart
10	chr22:32355000-32366400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr22:32365600-32366400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr22:32365600-32366600	Enhancers	Fetal Thymus	thymus
13	chr22:32365800-32366400	Enhancers	Primary hematopoietic stem cells	blood
14	chr22:32365800-32366400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr22:32365800-32366400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr22:32365800-32367200	Enhancers	Fetal Brain Male	brain
17	chr22:32365800-32367200	Flanking Active TSS	GM12878-XiMat	blood
18	chr22:32366000-32366400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr22:32366000-32366400	Enhancers	Primary T cells from cord blood	blood
20	chr22:32366000-32366400	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr22:32366000-32366400	Enhancers	Esophagus	oesophagus
22	chr22:32366000-32366400	Enhancers	Fetal Intestine Small	intestine
23	chr22:32366000-32366400	Enhancers	Gastric	stomach
24	chr22:32366000-32366400	Enhancers	Pancreas	Pancrea
25	chr22:32366000-32366400	Flanking Active TSS	HepG2	liver
26	chr22:32366000-32366600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr22:32366000-32366600	Enhancers	Primary B cells from cord blood	blood
28	chr22:32366000-32366600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr22:32366000-32366600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr22:32366000-32366600	Flanking Active TSS	Stomach Mucosa	stomach
31	chr22:32366000-32366800	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr22:32366000-32366800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr22:32366000-32366800	Enhancers	Fetal Lung	lung
34	chr22:32366000-32366800	Enhancers	Spleen	Spleen
35	chr22:32366000-32367000	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr22:32366000-32367000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr22:32366000-32367000	Active TSS	Hela-S3	cervix
38	chr22:32366000-32367200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:32366000-32367200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr22:32366000-32367200	Flanking Active TSS	HMEC	breast
41	chr22:32366000-32367400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr22:32366200-32366400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr22:32366200-32366400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr22:32366200-32366400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:32366200-32366400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:32366200-32366400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr22:32366200-32366400	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr22:32366200-32366400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr22:32366200-32366400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr22:32366200-32366400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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