Variant report

Variant	rs10400852
Chromosome Location	chr15:52393104-52393105
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	CBX3	chr15:52393009-52393393	K562	blood:	n/a	n/a
2	IRF4	chr15:52392536-52393336	GM12878	blood:	n/a	n/a
3	ATF2	chr15:52392964-52393462	GM12878	blood:	n/a	n/a
4	EP300	chr15:52392637-52393256	GM12878	blood:	n/a	n/a
5	FOS	chr15:52393050-52393416	MCF10A-Er-Src	breast:	n/a	chr15:52393208-52393219 chr15:52393233-52393244
6	POLR2A	chr15:52392988-52393312	Hela-S3	cervix:	n/a	n/a
7	PBX3	chr15:52392997-52393460	SK-N-SH	brain:	n/a	n/a
8	IRF4	chr15:52392459-52393199	GM12878	blood:	n/a	n/a
9	BCL11A	chr15:52392660-52393367	GM12878	blood:	n/a	n/a
10	SP1	chr15:52392663-52393332	GM12878	blood:	n/a	n/a
11	RAD21	chr15:52393001-52393373	SK-N-SH_RA	brain:	n/a	n/a
12	CEBPB	chr15:52393035-52393389	Hela-S3	cervix:	n/a	n/a
13	FOSL1	chr15:52392996-52393533	HCT-116	colon:	n/a	chr15:52393233-52393244 chr15:52393208-52393219
14	EP300	chr15:52393069-52393322	K562	blood:	n/a	n/a
15	EP300	chr15:52392984-52393375	SK-N-SH_RA	brain:	n/a	n/a
16	BHLHE40	chr15:52392639-52393211	HepG2	liver:	n/a	n/a
17	TCF12	chr15:52392636-52393290	GM12878	blood:	n/a	n/a
18	FOSL2	chr15:52393014-52393387	HepG2	liver:	n/a	chr15:52393208-52393219
19	BCLAF1	chr15:52392922-52393434	GM12878	blood:	n/a	n/a
20	JUND	chr15:52392981-52393445	A549	lung:	n/a	chr15:52393233-52393244 chr15:52393208-52393219
21	STAT3	chr15:52393056-52393312	MCF10A-Er-Src	breast:	n/a	n/a
22	REST	chr15:52393015-52393289	PFSK-1	brain:	n/a	n/a
23	FOS	chr15:52392632-52393394	MCF10A-Er-Src	breast:	n/a	chr15:52393208-52393219 chr15:52393233-52393244
24	CHD2	chr15:52392484-52393310	GM12878	blood:	n/a	n/a
25	BATF	chr15:52392717-52393418	GM12878	blood:	n/a	n/a
26	ATF2	chr15:52392940-52393488	GM12878	blood:	n/a	n/a
27	RCOR1	chr15:52392838-52393280	GM12878	blood:	n/a	n/a
28	RELA	chr15:52392559-52393318	GM18951	blood:	n/a	n/a
29	JUND	chr15:52393036-52393389	HepG2	liver:	n/a	chr15:52393233-52393244 chr15:52393208-52393219
30	JUN	chr15:52393055-52393422	HUVEC	blood vessel:	n/a	chr15:52393208-52393219
31	FOSL1	chr15:52393038-52393416	K562	blood:	n/a	chr15:52393233-52393244 chr15:52393208-52393219
32	RCOR1	chr15:52393045-52393449	K562	blood:	n/a	n/a
33	MXI1	chr15:52392472-52393409	IMR90	lung:	n/a	n/a
34	PAX5	chr15:52392620-52393299	GM12878	blood:	n/a	n/a
35	MAX	chr15:52393039-52393319	K562	blood:	n/a	n/a
36	TCF7L2	chr15:52392578-52393315	Hela-S3	cervix:	n/a	n/a
37	EBF1	chr15:52392504-52393423	GM12878	blood:	n/a	n/a
38	MTA3	chr15:52392927-52393644	GM12878	blood:	n/a	n/a
39	BATF	chr15:52392995-52393386	GM12878	blood:	n/a	n/a
40	NFIC	chr15:52392504-52393491	GM12878	blood:	n/a	n/a
41	FOS	chr15:52393031-52393575	HUVEC	blood vessel:	n/a	chr15:52393208-52393219 chr15:52393233-52393244
42	SP1	chr15:52392636-52393344	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:52392550-52393322	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:52392619-52393384	GM12878	blood:	n/a	n/a
45	JUND	chr15:52392929-52393557	SK-N-SH	brain:	n/a	chr15:52393233-52393244 chr15:52393208-52393219
46	EP300	chr15:52392990-52393327	SK-N-SH_RA	brain:	n/a	n/a
47	JUN	chr15:52393065-52393391	K562	blood:	n/a	chr15:52393208-52393219
48	BHLHE40	chr15:52392402-52393433	GM12878	blood:	n/a	n/a
49	NFIC	chr15:52393022-52393510	ECC-1	luminal epithelium:	n/a	n/a
50	MYC	chr15:52392624-52393312	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52385731..52388322-chr15:52391743..52394058,2	MCF-7	breast:
2	chr15:52309194..52314432-chr15:52385325..52393461,10	MCF-7	breast:
3	chr15:52361939..52363808-chr15:52392804..52395653,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259712	TF binding region
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000242327	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs16953085	1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs7163133	1.00[EUR][1000 genomes]
rs7164357	1.00[EUR][1000 genomes]
rs7165157	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	1.00[EUR][1000 genomes]
rs73402803	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402824	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402826	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	1.00[EUR][1000 genomes]
rs73402853	1.00[EUR][1000 genomes]
rs73402859	1.00[EUR][1000 genomes]
rs73402869	1.00[EUR][1000 genomes]
rs73402879	1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	1.00[EUR][1000 genomes]
rs8035146	1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041042	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041128	1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52385800-52395400	Weak transcription	Fetal Kidney	kidney
2	chr15:52386200-52399000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52387600-52395200	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:52387600-52395400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:52387600-52395400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:52387600-52396600	Weak transcription	Spleen	Spleen
7	chr15:52387600-52396800	Weak transcription	Esophagus	oesophagus
8	chr15:52388000-52393200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:52391800-52393200	Flanking Active TSS	Hela-S3	cervix
10	chr15:52391800-52397000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:52391800-52397000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr15:52392200-52395400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:52392200-52400800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:52392400-52393200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr15:52392400-52393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:52392400-52393400	Flanking Active TSS	GM12878-XiMat	blood
17	chr15:52392400-52393600	Enhancers	NHLF	lung
18	chr15:52392400-52394200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:52392400-52394800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr15:52392400-52394800	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr15:52392400-52396800	Enhancers	A549	lung
22	chr15:52392400-52397000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:52392400-52397000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:52392400-52397000	Enhancers	NHDF-Ad	bronchial
25	chr15:52392400-52398600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:52392600-52393200	Enhancers	Ovary	ovary
27	chr15:52392600-52393200	Flanking Active TSS	HepG2	liver
28	chr15:52392600-52393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:52392600-52393400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:52392600-52393400	Enhancers	Fetal Thymus	thymus
31	chr15:52392600-52393400	Enhancers	Osteobl	bone
32	chr15:52392600-52393600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:52392600-52393600	Enhancers	Fetal Muscle Leg	muscle
34	chr15:52392600-52393600	Enhancers	K562	blood
35	chr15:52392600-52393800	Enhancers	NH-A	brain
36	chr15:52392600-52394000	Enhancers	Fetal Muscle Trunk	muscle
37	chr15:52392600-52394600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr15:52392600-52396200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr15:52392600-52398600	Enhancers	HMEC	breast
40	chr15:52392600-52398600	Enhancers	NHEK	skin
41	chr15:52392800-52393400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr15:52392800-52393400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr15:52392800-52393600	Enhancers	Adipose Nuclei	Adipose
44	chr15:52392800-52396200	Enhancers	HUVEC	blood vessel
45	chr15:52393000-52393200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr15:52393000-52393200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:52393000-52393200	Enhancers	Right Atrium	heart
48	chr15:52393000-52393200	Enhancers	Small Intestine	intestine
49	chr15:52393000-52393400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:52393000-52393400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links