Variant report

Variant	rs2277445
Chromosome Location	chr13:52024936-52024937
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:52023042-52028956	GM12878	blood:	n/a	n/a
2	CHD1	chr13:52024742-52028646	IMR90	lung:	n/a	n/a
3	POLR2A	chr13:52024748-52024940	GM12891	blood:	n/a	n/a
4	POLR2A	chr13:52024109-52028486	GM18505	blood:	n/a	n/a
5	POLR2A	chr13:52023653-52028418	HepG2	liver:	n/a	n/a
6	POLR2A	chr13:52024147-52025024	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr13:52024356-52028620	GM12878	blood:	n/a	n/a
8	POLR2A	chr13:52024418-52024954	GM12891	blood:	n/a	n/a
9	POLR2A	chr13:52022995-52025001	HepG2	liver:	n/a	n/a
10	POLR2A	chr13:52024349-52028618	GM12878	blood:	n/a	n/a
11	POLR2A	chr13:52024561-52024953	GM12892	blood:	n/a	n/a
12	ZNF274	chr13:52024378-52025056	K562	blood:	n/a	n/a
13	HEY1	chr13:52024549-52024938	HepG2	liver:	n/a	n/a
14	POLR2A	chr13:52022043-52024987	K562	blood:	n/a	n/a
15	MXI1	chr13:52024891-52028769	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr13:52024592-52024951	MCF-7	breast:	n/a	n/a
17	POLR2A	chr13:52022607-52024992	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr13:52022978-52024990	HepG2	liver:	n/a	n/a
19	EP300	chr13:52024881-52025064	K562	blood:	n/a	n/a
20	POLR2A	chr13:52022300-52029025	GM12878	blood:	n/a	n/a
21	POLR2A	chr13:52023377-52029022	IMR90	lung:	n/a	n/a
22	POLR2A	chr13:52024582-52024986	GM12892	blood:	n/a	n/a
23	POLR2A	chr13:52023273-52029011	GM12891	blood:	n/a	n/a
24	POLR2A	chr13:52022966-52025095	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52022728..52028464-chr13:52376436..52381467,17	K562	blood:
2	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
3	chr13:52022475..52029228-chr13:52156654..52162250,29	K562	blood:
4	chr13:51933288..51938259-chr13:52024808..52026901,4	K562	blood:
5	chr13:52022170..52025698-chr13:52211557..52214174,3	MCF-7	breast:
6	chr13:52024267..52031024-chr13:52038927..52044194,9	MCF-7	breast:
7	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
8	chr13:52023587..52026212-chr20:45985508..45987866,2	MCF-7	breast:
9	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
10	chr13:51994030..51996463-chr13:52024763..52027853,3	MCF-7	breast:
11	chr13:52024284..52029908-chr13:52069886..52073128,6	K562	blood:
12	chr13:52023038..52025684-chr13:52169375..52171570,2	K562	blood:
13	chr13:52022042..52032158-chr13:52153162..52160287,46	K562	blood:
14	chr13:52022276..52028052-chr13:52350866..52359408,15	MCF-7	breast:
15	chr13:52023374..52025771-chr13:52171326..52173571,2	MCF-7	breast:
16	chr13:52024743..52028940-chr13:52112359..52118516,11	MCF-7	breast:
17	chr13:52024180..52026043-chr13:52139073..52141757,2	K562	blood:
18	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
19	chr13:51970484..51973482-chr13:52022310..52025240,2	K562	blood:
20	chr13:52015950..52029988-chr13:52150583..52166755,85	MCF-7	breast:

No data

Variant related genes	Relation type
RPS4XP16	TF binding region
INTS6-AS1	TF binding region
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000243900	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000229906	Chromatin interaction
ENSG00000224451	Chromatin interaction
ENSG00000269965	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000270101	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000252141	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1970132	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2408364	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2897913	1.00[YRI][hapmap]
rs3930275	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4409985	0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7322726	0.94[AFR][1000 genomes]
rs7323366	0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7325241	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7329338	0.81[JPT][hapmap];0.94[AFR][1000 genomes]
rs7991492	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7992256	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526753	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526762	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526767	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526770	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535647	1.00[YRI][hapmap]
rs9535666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535695	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568611	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3421830	chr13:52024776-52027324	Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51949400-52025000	Weak transcription	Fetal Muscle Leg	muscle
2	chr13:51950000-52025200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr13:51971800-52025000	Weak transcription	Fetal Stomach	stomach
4	chr13:51992400-52025400	Weak transcription	Esophagus	oesophagus
5	chr13:51995600-52025000	Weak transcription	Right Ventricle	heart
6	chr13:51995600-52025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:51997000-52025200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:52000600-52025200	Weak transcription	Small Intestine	intestine
9	chr13:52004600-52025200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr13:52012200-52025400	Weak transcription	Left Ventricle	heart
11	chr13:52013600-52025400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:52015000-52025000	Weak transcription	Brain Germinal Matrix	brain
13	chr13:52016800-52025200	Weak transcription	Psoas Muscle	Psoas
14	chr13:52017000-52025400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:52018800-52025200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:52019600-52025400	Weak transcription	Fetal Brain Male	brain
17	chr13:52020000-52025000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:52020000-52025000	Strong transcription	HSMM	muscle
19	chr13:52020400-52025000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:52020600-52025200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:52022200-52025000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:52022400-52025000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:52022600-52025200	Strong transcription	Placenta	Placenta
24	chr13:52023000-52025000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr13:52023000-52025000	Strong transcription	Fetal Thymus	thymus
26	chr13:52023000-52025200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr13:52023200-52025000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr13:52023200-52025000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr13:52023200-52025200	Genic enhancers	Primary B cells from cord blood	blood
30	chr13:52023200-52025200	Genic enhancers	Primary hematopoietic stem cells	blood
31	chr13:52023200-52025200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:52023400-52025000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr13:52023400-52025000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr13:52023400-52025000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr13:52023400-52025000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:52023400-52025000	Strong transcription	Fetal Kidney	kidney
37	chr13:52023400-52025000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
38	chr13:52023400-52025200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:52023400-52025200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr13:52023400-52025200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr13:52023400-52025200	Enhancers	Colon Smooth Muscle	Colon
42	chr13:52023600-52025200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr13:52023600-52025200	Genic enhancers	Liver	Liver
44	chr13:52023600-52025400	Weak transcription	Pancreas	Pancrea
45	chr13:52023800-52025000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr13:52023800-52025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr13:52023800-52025000	Enhancers	Hela-S3	cervix
48	chr13:52023800-52025200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr13:52023800-52025400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr13:52023800-52025600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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