Variant report

Variant	rs62137006
Chromosome Location	chr2:48572417-48572418
allele	C/T
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	FOSL2	chr2:48572132-48572896	A549	lung:	n/a	n/a
2	FOSL2	chr2:48572386-48572707	HepG2	liver:	n/a	n/a
3	CEBPB	chr2:48572385-48572757	IMR90	lung:	n/a	n/a
4	CEBPB	chr2:48572336-48572694	HepG2	liver:	n/a	n/a
5	ZBTB7A	chr2:48572374-48572567	HepG2	liver:	n/a	n/a
6	FOXA1	chr2:48572274-48572755	HepG2	liver:	n/a	n/a
7	FOXA1	chr2:48572335-48572691	HepG2	liver:	n/a	n/a
8	RCOR1	chr2:48572350-48572668	HepG2	liver:	n/a	n/a
9	FOXA1	chr2:48572294-48572637	HepG2	liver:	n/a	n/a
10	SP1	chr2:48572185-48572726	HepG2	liver:	n/a	n/a
11	CEBPB	chr2:48572192-48572830	A549	lung:	n/a	n/a
12	EP300	chr2:48572299-48572697	HepG2	liver:	n/a	chr2:48572348-48572362
13	FOXA2	chr2:48570899-48573824	HepG2	liver:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
14	JUN	chr2:48572359-48572718	HepG2	liver:	n/a	n/a
15	NFIC	chr2:48572323-48572717	HepG2	liver:	n/a	n/a
16	ARID3A	chr2:48572216-48572796	HepG2	liver:	n/a	n/a
17	HDAC2	chr2:48572291-48572664	HepG2	liver:	n/a	n/a
18	FOXA1	chr2:48572225-48572774	HepG2	liver:	n/a	n/a
19	FOSL2	chr2:48572322-48572649	HepG2	liver:	n/a	n/a
20	MYBL2	chr2:48571876-48572874	HepG2	liver:	n/a	n/a
21	CEBPB	chr2:48572296-48572718	A549	lung:	n/a	n/a
22	SMC3	chr2:48572300-48572658	HepG2	liver:	n/a	n/a
23	HNF4A	chr2:48572229-48572700	HepG2	liver:	n/a	chr2:48572517-48572532
24	EP300	chr2:48572185-48572794	A549	lung:	n/a	chr2:48572199-48572213 chr2:48572348-48572362
25	HNF4G	chr2:48572186-48572740	HepG2	liver:	n/a	chr2:48572516-48572531
26	CEBPB	chr2:48572377-48572646	HepG2	liver:	n/a	n/a
27	CEBPB	chr2:48572367-48572729	Hela-S3	cervix:	n/a	n/a
28	CEBPD	chr2:48572399-48572676	HepG2	liver:	n/a	n/a
29	HDAC2	chr2:48572288-48572716	HepG2	liver:	n/a	n/a
30	EP300	chr2:48572238-48572643	HepG2	liver:	n/a	chr2:48572348-48572362
31	SP1	chr2:48572168-48572838	A549	lung:	n/a	n/a
32	ZBTB7A	chr2:48572368-48572589	HepG2	liver:	n/a	n/a
33	TCF12	chr2:48572160-48572785	A549	lung:	n/a	n/a
34	MBD4	chr2:48572074-48572828	HepG2	liver:	n/a	n/a
35	NR3C1	chr2:48572352-48572695	A549	lung:	n/a	n/a
36	HNF4G	chr2:48572316-48572709	HepG2	liver:	n/a	chr2:48572516-48572531
37	HNF4A	chr2:48572308-48572725	HepG2	liver:	n/a	chr2:48572517-48572532
38	EP300	chr2:48572213-48572713	HepG2	liver:	n/a	chr2:48572348-48572362
39	CEBPB	chr2:48572366-48572575	HepG2	liver:	n/a	n/a
40	CHD2	chr2:48572280-48572576	HepG2	liver:	n/a	n/a
41	FOSL2	chr2:48572376-48572693	A549	lung:	n/a	n/a
42	NFIC	chr2:48571879-48572877	HepG2	liver:	n/a	n/a
43	ELF1	chr2:48572280-48572598	HepG2	liver:	n/a	n/a
44	HEY1	chr2:48572185-48572596	HepG2	liver:	n/a	n/a
45	CEBPB	chr2:48572340-48572798	HepG2	liver:	n/a	n/a
46	FOS	chr2:48572399-48572725	MCF10A-Er-Src	breast:	n/a	n/a
47	NR2F2	chr2:48572189-48572766	HepG2	liver:	n/a	n/a
48	HNF4A	chr2:48572332-48572668	HepG2	liver:	n/a	chr2:48572517-48572532
49	FOXA2	chr2:48572384-48572662	HepG2	liver:	n/a	n/a
50	CEBPB	chr2:48572348-48572727	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48541369..48544104-chr2:48569607..48573166,3	MCF-7	breast:
2	chr2:48566382..48569170-chr2:48571400..48573761,2	K562	blood:

Variant related genes	Relation type
RNU4-49P	TF binding region
ENSG00000251889	Chromatin interaction
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10153773	0.94[ASN][1000 genomes]
rs10174717	0.92[ASN][1000 genomes]
rs10180295	0.88[ASN][1000 genomes]
rs10186237	0.88[ASN][1000 genomes]
rs10193072	0.88[ASN][1000 genomes]
rs10199431	0.96[ASN][1000 genomes]
rs10208124	0.88[ASN][1000 genomes]
rs11676168	0.92[ASN][1000 genomes]
rs11682044	0.89[ASN][1000 genomes]
rs11690748	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12616792	0.82[ASN][1000 genomes]
rs12713008	0.82[ASN][1000 genomes]
rs13003076	0.87[ASN][1000 genomes]
rs13383364	0.88[ASN][1000 genomes]
rs13385535	0.92[ASN][1000 genomes]
rs13386751	0.86[ASN][1000 genomes]
rs13387171	0.88[ASN][1000 genomes]
rs13388291	0.88[ASN][1000 genomes]
rs13426834	0.86[ASN][1000 genomes]
rs13432998	0.87[ASN][1000 genomes]
rs2471405	0.83[ASN][1000 genomes]
rs28806843	0.87[ASN][1000 genomes]
rs28841370	1.00[ASN][1000 genomes]
rs4290706	0.89[ASN][1000 genomes]
rs4411759	0.92[ASN][1000 genomes]
rs4547573	0.86[ASN][1000 genomes]
rs4641990	0.91[ASN][1000 genomes]
rs56352447	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57537506	0.86[AFR][1000 genomes]
rs57668696	0.97[ASN][1000 genomes]
rs57893565	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58660534	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59264464	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59412192	0.88[ASN][1000 genomes]
rs59761994	0.99[ASN][1000 genomes]
rs60677957	0.85[ASN][1000 genomes]
rs62136987	0.99[ASN][1000 genomes]
rs62137001	0.99[ASN][1000 genomes]
rs62137002	0.99[ASN][1000 genomes]
rs62137003	0.99[ASN][1000 genomes]
rs62137005	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs62137007	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62137008	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137009	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62138801	0.88[ASN][1000 genomes]
rs6545027	0.86[ASN][1000 genomes]
rs6545028	0.86[ASN][1000 genomes]
rs6545029	0.80[ASN][1000 genomes]
rs6545030	0.94[ASN][1000 genomes]
rs6545034	0.97[ASN][1000 genomes]
rs6545035	0.97[ASN][1000 genomes]
rs6712029	0.94[ASN][1000 genomes]
rs6757206	0.86[ASN][1000 genomes]
rs72818493	0.89[ASN][1000 genomes]
rs72820405	0.99[ASN][1000 genomes]
rs72820418	0.84[AFR][1000 genomes]
rs72887649	0.89[ASN][1000 genomes]
rs7340322	0.83[ASN][1000 genomes]
rs7568960	0.85[ASN][1000 genomes]
rs7574125	0.92[ASN][1000 genomes]
rs9309152	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48553400-48574400	Weak transcription	Lung	lung
2	chr2:48557000-48573200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:48557000-48573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:48559800-48573400	Weak transcription	Fetal Kidney	kidney
5	chr2:48559800-48573400	Weak transcription	Right Atrium	heart
6	chr2:48560600-48573600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:48562000-48573400	Weak transcription	Psoas Muscle	Psoas
8	chr2:48562000-48573400	Weak transcription	K562	blood
9	chr2:48564800-48574400	Weak transcription	Fetal Stomach	stomach
10	chr2:48566600-48573600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:48569000-48573400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:48569000-48573400	Weak transcription	Brain Germinal Matrix	brain
13	chr2:48569000-48573400	Weak transcription	Fetal Lung	lung
14	chr2:48569000-48573400	Weak transcription	Pancreas	Pancrea
15	chr2:48569000-48574400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:48569200-48573400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:48570200-48572600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr2:48570600-48573400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:48570600-48573600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:48570800-48573400	Weak transcription	Placenta	Placenta
22	chr2:48570800-48575600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:48570800-48577400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:48571000-48573400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:48571000-48573400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:48571000-48573400	Weak transcription	Left Ventricle	heart
27	chr2:48571000-48574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:48571000-48574400	Weak transcription	Small Intestine	intestine
29	chr2:48571000-48577000	Weak transcription	Spleen	Spleen
30	chr2:48571200-48574800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
32	chr2:48571400-48572600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:48571400-48573400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:48571400-48573400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:48571600-48572600	Flanking Active TSS	A549	lung
36	chr2:48571600-48573400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:48571600-48573400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:48571600-48573600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:48571600-48573600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:48571600-48580000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:48571800-48572600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:48571800-48572600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:48571800-48572600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr2:48571800-48572800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr2:48571800-48572800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:48571800-48573000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:48571800-48573200	Enhancers	Primary B cells from cord blood	blood
48	chr2:48571800-48573200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:48571800-48573200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:48571800-48573200	Weak transcription	Colon Smooth Muscle	Colon

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