Variant report

Variant	rs9596514
Chromosome Location	chr13:52024417-52024418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr13:52024375-52024553	GM12878	blood:	n/a	n/a
2	POLR2A	chr13:52023042-52028956	GM12878	blood:	n/a	n/a
3	KAP1	chr13:52024365-52024896	K562	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	chr13:52024325-52024933	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr13:52022995-52025001	HepG2	liver:	n/a	n/a
10	POLR2A	chr13:52024047-52024541	HepG2	liver:	n/a	n/a
11	POLR2A	chr13:52024349-52028618	GM12878	blood:	n/a	n/a
12	POLR2A	chr13:52023930-52024691	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr13:52024380-52024894	GM12891	blood:	n/a	n/a
14	ZNF274	chr13:52024378-52025056	K562	blood:	n/a	n/a
15	POLR2A	chr13:52022043-52024987	K562	blood:	n/a	n/a
16	POLR2A	chr13:52022607-52024992	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr13:52022978-52024990	HepG2	liver:	n/a	n/a
18	POLR2A	chr13:52022300-52029025	GM12878	blood:	n/a	n/a
19	POLR2A	chr13:52023377-52029022	IMR90	lung:	n/a	n/a
20	POLR2A	chr13:52023273-52029011	GM12891	blood:	n/a	n/a
21	POLR2A	chr13:52022966-52025095	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:18 , 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	chr13:52022170..52025698-chr13:52211557..52214174,3	MCF-7	breast:
5	chr13:52024267..52031024-chr13:52038927..52044194,9	MCF-7	breast:
6	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
7	chr13:52023587..52026212-chr20:45985508..45987866,2	MCF-7	breast:
8	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
9	chr13:52024284..52029908-chr13:52069886..52073128,6	K562	blood:
10	chr13:52023038..52025684-chr13:52169375..52171570,2	K562	blood:
11	chr13:52022042..52032158-chr13:52153162..52160287,46	K562	blood:
12	chr13:52022276..52028052-chr13:52350866..52359408,15	MCF-7	breast:
13	chr13:52023374..52025771-chr13:52171326..52173571,2	MCF-7	breast:
14	chr13:52024180..52026043-chr13:52139073..52141757,2	K562	blood:
15	chr13:52023012..52024610-chr13:52355811..52358608,2	MCF-7	breast:
16	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
17	chr13:51970484..51973482-chr13:52022310..52025240,2	K562	blood:
18	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
ENSG00000252141	Chromatin interaction
ENSG00000229906	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000243900	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000224451	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12323252	1.00[AMR][1000 genomes]
rs55678657	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74084824	1.00[AMR][1000 genomes]
rs74084851	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74084865	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74084870	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9285178	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs9535670	0.81[YRI][hapmap]
rs9568600	0.81[YRI][hapmap]
rs9591404	1.00[AMR][1000 genomes]
rs9591406	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596511	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596515	1.00[AMR][1000 genomes]
rs9596525	1.00[AMR][1000 genomes]

No data

Chromatin state (count:114 , 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	chr13:51963200-52024800	Weak transcription	Fetal Intestine Large	intestine
4	chr13:51971800-52025000	Weak transcription	Fetal Stomach	stomach
5	chr13:51984400-52024800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:51992400-52025400	Weak transcription	Esophagus	oesophagus
7	chr13:51995400-52024600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr13:51995600-52025000	Weak transcription	Right Ventricle	heart
9	chr13:51995600-52025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:51997000-52025200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr13:52000600-52025200	Weak transcription	Small Intestine	intestine
12	chr13:52001400-52024600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:52003800-52024600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:52004200-52024800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:52004400-52024600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr13:52004600-52024800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr13:52004600-52025200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr13:52012200-52025400	Weak transcription	Left Ventricle	heart
19	chr13:52013600-52025400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:52015000-52025000	Weak transcription	Brain Germinal Matrix	brain
21	chr13:52016800-52025200	Weak transcription	Psoas Muscle	Psoas
22	chr13:52017000-52025400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:52018800-52024800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr13:52018800-52025200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr13:52019600-52025400	Weak transcription	Fetal Brain Male	brain
26	chr13:52019800-52024600	Weak transcription	Brain Angular Gyrus	brain
27	chr13:52020000-52025000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr13:52020000-52025000	Strong transcription	HSMM	muscle
29	chr13:52020400-52024800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr13:52020400-52025000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:52020600-52025200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:52022200-52024600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr13:52022200-52025000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:52022400-52024600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr13:52022400-52024800	Weak transcription	Brain Substantia Nigra	brain
36	chr13:52022400-52025000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr13:52022600-52024600	Strong transcription	HMEC	breast
38	chr13:52022600-52025200	Strong transcription	Placenta	Placenta
39	chr13:52022800-52024800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:52023000-52024600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr13:52023000-52024600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr13:52023000-52024600	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr13:52023000-52024600	Strong transcription	NHDF-Ad	bronchial
44	chr13:52023000-52025000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr13:52023000-52025000	Strong transcription	Fetal Thymus	thymus
46	chr13:52023000-52025200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:52023200-52024600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr13:52023200-52024600	Genic enhancers	HepG2	liver
49	chr13:52023200-52025000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:52023200-52025000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links