Variant report

Variant	rs58280122
Chromosome Location	chr2:234260231-234260232
allele	A/C
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	FOS	chr2:234260167-234260391	MCF10A-Er-Src	breast:	n/a	n/a
2	BHLHE40	chr2:234260043-234260428	K562	blood:	n/a	n/a
3	USF2	chr2:234260195-234260286	K562	blood:	n/a	chr2:234260225-234260236
4	USF1	chr2:234259973-234260462	HCT-116	colon:	n/a	n/a
5	USF1	chr2:234260118-234260399	SK-N-SH_RA	brain:	n/a	n/a
6	CUX1	chr2:234260141-234260360	K562	blood:	n/a	n/a
7	STAT3	chr2:234259351-234260392	MCF10A-Er-Src	breast:	n/a	chr2:234259389-234259400 chr2:234259557-234259566
8	FOSL2	chr2:234259071-234260407	A549	lung:	n/a	chr2:234259569-234259578 chr2:234259568-234259580
9	KAP1	chr2:234259061-234260406	U2OS	brain:	n/a	n/a
10	MAFK	chr2:234260088-234260258	K562	blood:	n/a	n/a
11	USF1	chr2:234260026-234260394	A549	lung:	n/a	n/a
12	USF2	chr2:234260068-234260371	Hela-S3	cervix:	n/a	chr2:234260225-234260236
13	POLR2A	chr2:234259959-234260356	U87	brain:	n/a	n/a
14	ZMIZ1	chr2:234260116-234260316	K562	blood:	n/a	n/a
15	MAX	chr2:234260072-234260420	NB4	blood:	n/a	n/a
16	USF1	chr2:234260028-234260367	A549	lung:	n/a	n/a
17	JUN	chr2:234259297-234260416	K562	blood:	n/a	chr2:234259569-234259578 chr2:234259568-234259580
18	FOS	chr2:234260077-234260333	MCF10A-Er-Src	breast:	n/a	n/a
19	USF1	chr2:234260044-234260411	A549	lung:	n/a	n/a
20	USF1	chr2:234260068-234260423	SK-N-SH	brain:	n/a	n/a
21	USF1	chr2:234260068-234260442	K562	blood:	n/a	n/a
22	SP1	chr2:234258928-234260358	HCT-116	colon:	n/a	n/a
23	FOSL1	chr2:234259052-234260433	HCT-116	colon:	n/a	chr2:234259556-234259567 chr2:234259569-234259578 chr2:234259568-234259579 chr2:234259568-234259580
24	STAT3	chr2:234259375-234260400	MCF10A-Er-Src	breast:	n/a	chr2:234259389-234259400 chr2:234259557-234259566
25	FOSL1	chr2:234258935-234260437	HCT-116	colon:	n/a	chr2:234259556-234259567 chr2:234259569-234259578 chr2:234259568-234259579 chr2:234259568-234259580
26	JUND	chr2:234258937-234260490	HCT-116	colon:	n/a	chr2:234259569-234259578 chr2:234259568-234259579 chr2:234259568-234259580 chr2:234259556-234259567
27	FOS	chr2:234259294-234260420	MCF10A-Er-Src	breast:	n/a	chr2:234259568-234259579 chr2:234259569-234259578 chr2:234259556-234259567 chr2:234259568-234259580
28	JUND	chr2:234259271-234260455	K562	blood:	n/a	chr2:234259569-234259578 chr2:234259568-234259579 chr2:234259568-234259580 chr2:234259556-234259567
29	STAT3	chr2:234259402-234260298	MCF10A-Er-Src	breast:	n/a	chr2:234259557-234259566
30	USF1	chr2:234260116-234260350	SK-N-SH_RA	brain:	n/a	n/a
31	EP300	chr2:234260109-234260370	K562	blood:	n/a	n/a
32	RCOR1	chr2:234260083-234260468	K562	blood:	n/a	n/a
33	POLR2A	chr2:234260056-234260414	U87	brain:	n/a	n/a
34	MYC	chr2:234259147-234260355	K562	blood:	n/a	chr2:234259570-234259579
35	MYC	chr2:234260075-234260350	MCF10A-Er-Src	breast:	n/a	n/a
36	USF1	chr2:234260083-234260405	K562	blood:	n/a	n/a
37	POLR2A	chr2:234260021-234260525	U87	brain:	n/a	n/a
38	FOS	chr2:234259284-234260399	MCF10A-Er-Src	breast:	n/a	chr2:234259568-234259579 chr2:234259569-234259578 chr2:234259556-234259567 chr2:234259568-234259580
39	USF1	chr2:234259852-234260472	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234257933..234260937-chr2:234261415..234264229,3	K562	blood:
2	chr2:234252596..234255070-chr2:234259544..234261790,2	MCF-7	breast:
3	chr2:234250454..234252817-chr2:234259507..234261649,2	MCF-7	breast:
4	chr2:234258654..234260896-chr2:234262665..234264444,3	MCF-7	breast:
5	chr2:234259457..234261123-chr2:234261520..234263458,2	MCF-7	breast:
6	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:
7	chr2:234196279..234198158-chr2:234258001..234260532,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP40-1	chr2:234259778-234262062	ENSG00000259793.1
2	lnc-USP40-1	chr2:234259778-234260434	NONHSAT077479

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000243637	TF binding region
ENSG00000077044	Chromatin interaction
ENSG00000251791	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000130561	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1046976	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675531	0.95[EUR][1000 genomes]
rs11679008	0.95[EUR][1000 genomes]
rs13384918	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420688	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55684040	0.95[EUR][1000 genomes]
rs55693723	0.95[EUR][1000 genomes]
rs55804614	0.95[EUR][1000 genomes]
rs55893802	0.92[EUR][1000 genomes]
rs56082182	0.95[EUR][1000 genomes]
rs56405280	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72978363	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72978374	0.95[EUR][1000 genomes]
rs72978375	0.95[EUR][1000 genomes]
rs72980318	0.94[EUR][1000 genomes]
rs7573866	0.95[EUR][1000 genomes]
rs7598771	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234255800-234262400	Weak transcription	Right Atrium	heart
2	chr2:234256200-234260800	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:234256400-234260400	Enhancers	Fetal Intestine Small	intestine
4	chr2:234256400-234262400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr2:234256600-234261400	Enhancers	Primary B cells from cord blood	blood
6	chr2:234256800-234262400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:234257000-234262200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:234257200-234260400	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:234257400-234260400	Enhancers	Fetal Intestine Large	intestine
10	chr2:234257600-234260400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:234257800-234260400	Enhancers	K562	blood
12	chr2:234257800-234263000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr2:234258000-234260400	Enhancers	HSMM	muscle
14	chr2:234258000-234261800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:234258200-234260800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:234258200-234261200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:234258200-234261800	Weak transcription	Esophagus	oesophagus
18	chr2:234258200-234261800	Weak transcription	Lung	lung
19	chr2:234258200-234262000	Weak transcription	Right Ventricle	heart
20	chr2:234258200-234262600	Weak transcription	Psoas Muscle	Psoas
21	chr2:234258400-234260400	Enhancers	Brain Anterior Caudate	brain
22	chr2:234258400-234261000	Enhancers	NHEK	skin
23	chr2:234258400-234261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:234258400-234261800	Weak transcription	Gastric	stomach
25	chr2:234258400-234261800	Weak transcription	Thymus	Thymus
26	chr2:234258400-234262000	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:234258400-234262200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:234258400-234262400	Weak transcription	Ovary	ovary
29	chr2:234258600-234260400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:234258600-234261400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:234258600-234261800	Weak transcription	Spleen	Spleen
32	chr2:234258600-234262000	Weak transcription	Adipose Nuclei	Adipose
33	chr2:234258600-234262000	Weak transcription	Brain Substantia Nigra	brain
34	chr2:234258600-234262200	Weak transcription	Primary T cells from cord blood	blood
35	chr2:234258600-234262400	Weak transcription	Fetal Kidney	kidney
36	chr2:234258800-234260400	Enhancers	HMEC	breast
37	chr2:234258800-234262600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:234259000-234260400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr2:234259000-234260400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:234259000-234260400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:234259000-234260400	Flanking Active TSS	A549	lung
42	chr2:234259200-234260400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:234259200-234260400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr2:234259200-234260400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:234259200-234260400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:234259200-234260400	Enhancers	HUVEC	blood vessel
47	chr2:234259200-234260400	Enhancers	NHDF-Ad	bronchial
48	chr2:234259200-234261800	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:234259200-234262400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:234259400-234260400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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