Variant report

Variant	rs17402569
Chromosome Location	chr15:49915406-49915407
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	POLR2A	chr15:49911978-49916148	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr15:49911990-49915525	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr15:49915259-49915968	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:49912375-49916243	ProgFib	skin:	n/a	n/a
5	POLR2A	chr15:49911535-49916197	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:49914708..49917210-chr15:49937827..49939413,2	MCF-7	breast:
2	chr15:49914376..49915416-chr15:50124445..50125402,4	MCF-7	breast:
3	chr14:25147349..25148317-chr15:49914642..49915614,2	MCF-7	breast:

Variant related genes	Relation type
FAM227B	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10519233	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070707	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12901416	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs12902107	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs12902794	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs13329455	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354918	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395900	0.85[EUR][1000 genomes]
rs1546424	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1546425	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1588127	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17404262	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17480434	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481696	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483139	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413947	0.83[EUR][1000 genomes]
rs2413963	0.86[CEU][hapmap]
rs28393768	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28408092	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28409376	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28430272	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28465200	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484276	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28492008	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28516445	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568399	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635979	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669217	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28671247	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28798135	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28843724	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3210227	0.90[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774539	0.84[CEU][hapmap]
rs8034473	0.85[EUR][1000 genomes]
rs8038373	0.81[EUR][1000 genomes]
rs8040436	0.86[CEU][hapmap]
rs8040716	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs967892	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs967893	0.86[CEU][hapmap]
rs9920033	1.00[YRI][hapmap]
rs9920574	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920705	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569392	chr15:49789413-49926300	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 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	chr15:49911400-49916000	Active TSS	Stomach Smooth Muscle	stomach
2	chr15:49911600-49916600	Active TSS	GM12878-XiMat	blood
3	chr15:49912600-49915800	Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr15:49913600-49916600	Flanking Active TSS	Osteobl	bone
5	chr15:49913600-49937400	Weak transcription	Spleen	Spleen
6	chr15:49913800-49916200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:49913800-49916600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:49914000-49915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:49914000-49915600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:49914000-49915600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:49914000-49917000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:49914000-49917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:49914000-49917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:49914000-49917800	Weak transcription	Esophagus	oesophagus
15	chr15:49914000-49917800	Weak transcription	Left Ventricle	heart
16	chr15:49914000-49917800	Weak transcription	Lung	lung
17	chr15:49914000-49930000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:49914200-49916200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:49914200-49916200	Flanking Active TSS	NHDF-Ad	bronchial
20	chr15:49914200-49916600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr15:49914400-49915800	Enhancers	Primary hematopoietic stem cells	blood
22	chr15:49914400-49915800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:49914400-49916000	Enhancers	Brain Cingulate Gyrus	brain
24	chr15:49914400-49916000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr15:49914400-49916000	Enhancers	Fetal Muscle Leg	muscle
26	chr15:49914400-49916000	Enhancers	Psoas Muscle	Psoas
27	chr15:49914400-49916200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:49914400-49916200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:49914400-49916600	Enhancers	Primary T cells from cord blood	blood
30	chr15:49914400-49917400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:49914400-49917400	Weak transcription	Placenta	Placenta
32	chr15:49914400-49917600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:49914400-49917800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr15:49914400-49917800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:49914400-49917800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:49914400-49917800	Weak transcription	Aorta	Aorta
37	chr15:49914400-49917800	Weak transcription	Colonic Mucosa	Colon
38	chr15:49914400-49917800	Weak transcription	Fetal Intestine Large	intestine
39	chr15:49914400-49917800	Weak transcription	Gastric	stomach
40	chr15:49914400-49917800	Weak transcription	Right Ventricle	heart
41	chr15:49914400-49918000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:49914400-49918000	Weak transcription	Thymus	Thymus
43	chr15:49914400-49927200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:49914400-49936400	Weak transcription	Small Intestine	intestine
45	chr15:49914400-49938000	Weak transcription	Brain Substantia Nigra	brain
46	chr15:49914600-49915600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr15:49914600-49915600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr15:49914600-49915600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr15:49914600-49915800	Enhancers	Right Atrium	heart
50	chr15:49914600-49915800	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links