Variant report

Variant	rs56879885
Chromosome Location	chr2:48571636-48571637
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	TCF7L2	chr2:48570898-48571786	PANC-1	pancreas:	n/a	chr2:48571404-48571420 chr2:48571405-48571419 chr2:48571404-48571420
2	KAP1	chr2:48570881-48571860	HEK293	kidney:	n/a	chr2:48571522-48571531
3	MYBL2	chr2:48570798-48571818	HepG2	liver:	n/a	chr2:48571399-48571412
4	EP300	chr2:48571284-48571713	SK-N-SH_RA	brain:	n/a	n/a
5	SIN3AK20	chr2:48571258-48571692	A549	lung:	n/a	n/a
6	E2F4	chr2:48571433-48571671	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr2:48571350-48571769	MCF10A-Er-Src	breast:	n/a	chr2:48571519-48571530 chr2:48571521-48571529 chr2:48571522-48571529
8	TCF12	chr2:48570813-48571987	SK-N-SH	brain:	n/a	n/a
9	FOXM1	chr2:48571134-48571844	SK-N-SH	brain:	n/a	n/a
10	FOSL2	chr2:48571140-48571821	SK-N-SH	brain:	n/a	chr2:48571521-48571529 chr2:48571522-48571529
11	TCF7L2	chr2:48571268-48571677	MCF-7	breast:	n/a	chr2:48571404-48571420 chr2:48571405-48571419 chr2:48571404-48571420
12	MYC	chr2:48571024-48571710	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA2	chr2:48571278-48571870	A549	lung:	n/a	chr2:48571350-48571362
14	TCF12	chr2:48570574-48572155	A549	lung:	n/a	n/a
15	MBD4	chr2:48571113-48571997	HepG2	liver:	n/a	n/a
16	GATA3	chr2:48570616-48572011	SK-N-SH	brain:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
17	MXI1	chr2:48571355-48571732	HepG2	liver:	n/a	n/a
18	RXRA	chr2:48571189-48571886	SK-N-SH	brain:	n/a	chr2:48571521-48571530
19	FOXA1	chr2:48571291-48571671	HepG2	liver:	n/a	chr2:48571350-48571362
20	HDAC2	chr2:48571339-48571644	HepG2	liver:	n/a	chr2:48571414-48571428 chr2:48571467-48571476
21	NR3C1	chr2:48571124-48571751	A549	lung:	n/a	n/a
22	STAT3	chr2:48571461-48571695	MCF10A-Er-Src	breast:	n/a	n/a
23	REST	chr2:48570970-48571781	A549	lung:	n/a	n/a
24	GATA3	chr2:48571270-48571675	SH-SY5Y	brain:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
25	USF2	chr2:48571389-48571723	Hela-S3	cervix:	n/a	n/a
26	RUNX3	chr2:48571102-48571745	GM12878	blood:	n/a	n/a
27	KAP1	chr2:48570845-48571789	U2OS	brain:	n/a	chr2:48571522-48571531
28	NFIC	chr2:48571032-48571925	SK-N-SH	brain:	n/a	n/a
29	CEBPB	chr2:48570993-48571791	A549	lung:	n/a	n/a
30	JUND	chr2:48571348-48571662	A549	lung:	n/a	chr2:48571521-48571529 chr2:48571522-48571529
31	HDAC2	chr2:48571219-48571747	MCF-7	breast:	n/a	chr2:48571414-48571428 chr2:48571467-48571476
32	GATA3	chr2:48571082-48571758	MCF-7	breast:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
33	NFIC	chr2:48571228-48571747	SK-N-SH	brain:	n/a	n/a
34	FOXA1	chr2:48571073-48571808	HepG2	liver:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
35	GATA3	chr2:48570698-48571959	SK-N-SH	brain:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
36	JUND	chr2:48571099-48571865	SK-N-SH	brain:	n/a	chr2:48571521-48571529 chr2:48571522-48571529
37	CHD2	chr2:48571253-48571689	Hela-S3	cervix:	n/a	n/a
38	FOS	chr2:48571022-48571728	MCF10A-Er-Src	breast:	n/a	chr2:48571519-48571530 chr2:48571521-48571529 chr2:48571522-48571529
39	EP300	chr2:48571284-48571763	SK-N-SH_RA	brain:	n/a	n/a
40	TCF7L2	chr2:48571062-48571657	Hela-S3	cervix:	n/a	chr2:48571404-48571420 chr2:48571405-48571419 chr2:48571404-48571420
41	STAT3	chr2:48571056-48571754	Hela-S3	cervix:	n/a	chr2:48571385-48571396
42	FOXA2	chr2:48571096-48571813	A549	lung:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
43	SP1	chr2:48571172-48571790	A549	lung:	n/a	n/a
44	POLR2A	chr2:48571220-48571782	SK-N-SH	brain:	n/a	n/a
45	FOSL2	chr2:48571265-48571724	SK-N-SH	brain:	n/a	chr2:48571521-48571529 chr2:48571522-48571529
46	POLR2A	chr2:48570735-48571779	U87	brain:	n/a	n/a
47	MAX	chr2:48571279-48571742	SK-N-SH	brain:	n/a	n/a
48	GATA3	chr2:48570983-48571839	MCF-7	breast:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
49	FOXA2	chr2:48570899-48573824	HepG2	liver:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
50	SP1	chr2:48570675-48571831	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: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17037271	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28399967	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28439229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28570232	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595126	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34136171	0.85[EUR][1000 genomes]
rs57729372	0.87[AFR][1000 genomes]
rs60743061	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62137000	0.85[AFR][1000 genomes]
rs62138817	0.82[AFR][1000 genomes]
rs6545031	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545033	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737455	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72887650	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72887686	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7563625	0.83[AFR][1000 genomes]
rs7576648	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9677579	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][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	chr2:48565800-48571800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:48566600-48573600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:48569000-48573400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:48569000-48573400	Weak transcription	Brain Germinal Matrix	brain
14	chr2:48569000-48573400	Weak transcription	Fetal Lung	lung
15	chr2:48569000-48573400	Weak transcription	Pancreas	Pancrea
16	chr2:48569000-48574400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:48569200-48573400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:48570200-48572600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr2:48570600-48571800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:48570600-48572000	Enhancers	Primary B cells from peripheral blood	blood
22	chr2:48570600-48572000	Enhancers	Fetal Thymus	thymus
23	chr2:48570600-48572000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:48570600-48573400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:48570600-48573600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:48570800-48571800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr2:48570800-48571800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:48570800-48571800	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr2:48570800-48571800	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr2:48570800-48571800	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr2:48570800-48571800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr2:48570800-48572000	Flanking Active TSS	HUVEC	blood vessel
33	chr2:48570800-48572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:48570800-48572200	Enhancers	Fetal Intestine Large	intestine
35	chr2:48570800-48572400	Flanking Active TSS	HepG2	liver
36	chr2:48570800-48573400	Weak transcription	Placenta	Placenta
37	chr2:48570800-48575600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:48570800-48577400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:48571000-48571800	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr2:48571000-48571800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr2:48571000-48571800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:48571000-48571800	Active TSS	Aorta	Aorta
43	chr2:48571000-48571800	Flanking Active TSS	Liver	Liver
44	chr2:48571000-48571800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr2:48571000-48571800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:48571000-48571800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:48571000-48571800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr2:48571000-48571800	Flanking Active TSS	Dnd41	blood
49	chr2:48571000-48571800	Flanking Active TSS	HMEC	breast
50	chr2:48571000-48571800	Flanking Active TSS	NHEK	skin

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