Variant report

Variant	rs58952888
Chromosome Location	chr22:30476561-30476562
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr22:30476091-30476707	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUN	chr22:30476397-30476570	H1-hESC	embryonic stem cell:	n/a	n/a
3	POU2F2	chr22:30476019-30476561	GM12878	blood:	n/a	n/a
4	TBP	chr22:30476112-30476613	H1-hESC	embryonic stem cell:	n/a	n/a
5	RFX5	chr22:30476430-30476584	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr22:30476066-30476864	H1-hESC	embryonic stem cell:	n/a	chr22:30476599-30476608
7	POLR2A	chr22:30476323-30476580	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr22:30476054-30476731	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr22:30476364-30476641	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr22:30476353-30476576	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr22:30475991-30476719	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr22:30476060-30476646	H1-hESC	embryonic stem cell:	n/a	chr22:30476376-30476387
13	E2F6	chr22:30476053-30476683	H1-hESC	embryonic stem cell:	n/a	chr22:30476599-30476608
14	MAX	chr22:30476190-30476707	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr22:30476439-30476564	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr22:30476048-30476604	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:30476525-30476575	HIPEpiC	eye:	n/a
2	chr22:30476525-30476575	HRCEpiC	kidney:	n/a
3	chr22:30476525-30476575	NB4	blood:	n/a
4	chr22:30476525-30476575	MCF10A-Er-Src	breast:	n/a
5	chr22:30476525-30476575	BJ	skin:	n/a
6	chr22:30476525-30476575	HCPEpiC	choroid plexus:	n/a
7	chr22:30476525-30476575	HRE	kidney:	n/a
8	chr22:30476525-30476575	BE2_C	brain:	n/a
9	chr22:30476525-30476575	AG09319	gingival:	n/a
10	chr22:30476525-30476575	HepG2	liver:	n/a
11	chr22:30476525-30476575	HEK293	kidney:	embryo
12	chr22:30476525-30476575	AG04450	lung:	fetal
13	chr22:30476525-30476575	AG04449	skin:	fetal
14	chr22:30476525-30476575	GM19239	blood:	n/a
15	chr22:30476525-30476575	PrEC	prostate:	n/a
16	chr22:30476525-30476575	K562	blood:	n/a
17	chr22:30476525-30476575	HNPCEpiC	eye:	n/a
18	chr22:30476525-30476575	HUVEC	blood vessel:	n/a
19	chr22:30476525-30476575	T-47D	breast:	n/a
20	chr22:30476525-30476575	AG09309	skin:	n/a
21	chr22:30476525-30476575	RPTEC	kidney:	n/a
22	chr22:30476525-30476575	HCM	heart:	n/a
23	chr22:30476525-30476575	ProgFib	skin:	n/a
24	chr22:30476525-30476575	HPAEpiC	pulmonary alveolar:	n/a
25	chr22:30476525-30476575	SK-N-SH	brain:	n/a
26	chr22:30476525-30476575	NHDF-neo	bronchial:	n/a
27	chr22:30476525-30476575	ovcar-3	ovarian:	n/a
28	chr22:30476525-30476575	GM06990	blood:	n/a
29	chr22:30476525-30476575	SAEC	small airway:	n/a
30	chr22:30476525-30476575	HMEC	breast:	n/a
31	chr22:30476525-30476575	NHBE	bronchial:	n/a
32	chr22:30476525-30476575	GM12892	blood:	n/a
33	chr22:30476525-30476575	U87	brain:	n/a
34	chr22:30476525-30476575	H1-hESC	embryonic stem cell:	embryo
35	chr22:30476525-30476575	Caco-2	colon:	n/a
36	chr22:30476525-30476575	SK-N-MC	brain:	n/a
37	chr22:30476525-30476575	HAEpiC	amniotic membrane:	n/a
38	chr22:30476525-30476575	SK-N-SH_RA	brain:	n/a
39	chr22:30476525-30476575	ECC-1	luminal epithelium:	n/a
40	chr22:30476525-30476575	A549	lung:	n/a
41	chr22:30476525-30476575	NH-A	brain:	n/a
42	chr22:30476525-30476575	LNCaP	prostate:	n/a
43	chr22:30476525-30476575	HRPEpiC	eye:	n/a
44	chr22:30476525-30476575	MCF-7	breast:	n/a
45	chr22:30476525-30476575	Jurkat	blood:	n/a
46	chr22:30476525-30476575	Hepatocyte	liver:	n/a
47	chr22:30476525-30476575	AoSMC	blood vessel:	n/a
48	chr22:30476525-30476575	GM12878	blood:	n/a
49	chr22:30476525-30476575	CMK	blood:	n/a
50	chr22:30476525-30476575	HL-60	blood:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIF-2	chr22:30476117-30476884	NONHSAT084754
2	lnc-LIF-2	chr22:30476117-30476884	NONHSAT084756

No data

Variant related genes	Relation type
HORMAD2	TF binding region
ENSG00000227117	TF binding region
ENSG00000227117	CpG island
HORMAD2	CpG island

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs16988115	0.83[AMR][1000 genomes]
rs16988122	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16988151	0.83[AMR][1000 genomes]
rs56733052	0.83[AMR][1000 genomes]
rs57724305	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59580785	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs5997565	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6006297	0.83[AMR][1000 genomes]
rs6006299	0.83[AMR][1000 genomes]
rs6006301	0.83[AMR][1000 genomes]
rs6006309	0.83[AMR][1000 genomes]
rs6006317	0.83[AMR][1000 genomes]
rs6006318	0.83[AMR][1000 genomes]
rs6006331	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60964812	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61043203	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61191536	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73394876	0.83[AMR][1000 genomes]
rs73396842	0.83[AMR][1000 genomes]
rs73396845	0.83[AMR][1000 genomes]
rs73398604	0.83[AMR][1000 genomes]
rs73398637	0.83[AMR][1000 genomes]
rs73398640	0.83[AMR][1000 genomes]
rs73398663	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73400633	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73400648	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73400675	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73400689	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73402619	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73402627	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73402640	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73402644	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73402647	0.83[AMR][1000 genomes]
rs73402653	0.83[AMR][1000 genomes]
rs73402667	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30474400-30476600	Weak transcription	HepG2	liver
2	chr22:30475200-30476600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr22:30475400-30476600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr22:30475400-30476600	Enhancers	Fetal Brain Male	brain
5	chr22:30475600-30476600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr22:30475800-30476600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr22:30475800-30476600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr22:30475800-30476600	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr22:30475800-30476600	Bivalent/Poised TSS	Placenta	Placenta
10	chr22:30475800-30476800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr22:30475800-30476800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr22:30475800-30485400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:30476000-30476600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr22:30476000-30476600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr22:30476000-30476600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
17	chr22:30476000-30476600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr22:30476000-30476600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr22:30476000-30476600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr22:30476000-30476600	Active TSS	Psoas Muscle	Psoas
24	chr22:30476000-30476600	Active TSS	Right Atrium	heart
25	chr22:30476000-30476600	Active TSS	Right Ventricle	heart
26	chr22:30476000-30476600	Enhancers	Spleen	Spleen
27	chr22:30476000-30476600	Active TSS	Osteobl	bone
28	chr22:30476000-30476800	Active TSS	Brain Anterior Caudate	brain
29	chr22:30476000-30476800	Active TSS	Brain Germinal Matrix	brain
30	chr22:30476000-30476800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
31	chr22:30476000-30476800	Active TSS	Fetal Brain Female	brain
32	chr22:30476000-30477200	Active TSS	Brain Substantia Nigra	brain
33	chr22:30476200-30476600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
34	chr22:30476200-30476600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
35	chr22:30476200-30476600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
36	chr22:30476200-30476600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr22:30476200-30476600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr22:30476200-30476600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr22:30476200-30476600	Enhancers	Liver	Liver
40	chr22:30476200-30476600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
41	chr22:30476200-30476600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr22:30476200-30476600	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr22:30476200-30476600	ZNF genes & repeats	Lung	lung
44	chr22:30476200-30476600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
45	chr22:30476200-30476600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr22:30476200-30476800	Active TSS	Fetal Kidney	kidney
47	chr22:30476400-30476600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
48	chr22:30476400-30476600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr22:30476400-30476600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr22:30476400-30476600	Bivalent/Poised TSS	Brain Angular Gyrus	brain

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