Variant report

Variant	rs1912403
Chromosome Location	chr15:56208933-56208934
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	chr15:56208821-56209581	U87	brain:	n/a	n/a
2	STAT3	chr15:56208899-56209037	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr15:56207813-56210860	A549	lung:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
4	TCF12	chr15:56208460-56209717	A549	lung:	n/a	n/a
5	MAFK	chr15:56208832-56209524	IMR90	lung:	n/a	n/a
6	MYC	chr15:56208830-56209499	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr15:56208803-56209657	U87	brain:	n/a	n/a
8	POLR2A	chr15:56208392-56209563	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr15:56208830-56209657	U87	brain:	n/a	n/a
10	TCF12	chr15:56208835-56209657	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
NEDD4	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10518823	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12898478	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899701	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12901802	0.93[EUR][1000 genomes]
rs12902173	0.93[EUR][1000 genomes]
rs12904236	0.93[EUR][1000 genomes]
rs12906245	0.86[EUR][1000 genomes]
rs12906350	0.86[EUR][1000 genomes]
rs12908286	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908466	0.84[EUR][1000 genomes]
rs12911101	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12911380	0.83[AMR][1000 genomes]
rs12913220	0.86[EUR][1000 genomes]
rs17819216	1.00[MEX][hapmap]
rs17819270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912397	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899593	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs34162982	0.93[EUR][1000 genomes]
rs34223710	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34333169	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34652186	0.93[EUR][1000 genomes]
rs34718758	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34727807	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34995202	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35086304	0.93[EUR][1000 genomes]
rs35142499	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35313340	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35759462	0.86[EUR][1000 genomes]
rs4296197	0.93[EUR][1000 genomes]
rs66857236	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67046147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67825863	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71476753	0.93[EUR][1000 genomes]
rs71476755	0.93[EUR][1000 genomes]
rs71476760	0.93[EUR][1000 genomes]
rs7172454	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8038204	0.93[EUR][1000 genomes]
rs8039617	0.93[EUR][1000 genomes]
rs8042074	0.93[EUR][1000 genomes]
rs8042216	0.93[EUR][1000 genomes]
rs8043427	0.93[EUR][1000 genomes]
rs906811	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv569542	chr15:56185262-56210929	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv819986	chr15:56208434-56209256	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1912403	CYP19A1	cis	cerebellum	SCAN
rs1912403	UNC13C	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56176000-56216200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:56188600-56218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:56190000-56220000	Weak transcription	Pancreas	Pancrea
4	chr15:56190200-56221200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:56190400-56219800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:56192600-56209000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:56200200-56213200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:56200400-56209000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:56200800-56218000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:56201000-56230000	Weak transcription	Fetal Intestine Large	intestine
11	chr15:56201200-56217200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:56203600-56209600	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr15:56204600-56209800	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr15:56204800-56210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:56206800-56217800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:56207400-56209200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:56207400-56209400	Flanking Active TSS	Hela-S3	cervix
18	chr15:56207400-56209600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:56207400-56209600	Active TSS	Psoas Muscle	Psoas
20	chr15:56207400-56210000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:56207400-56210400	Weak transcription	Dnd41	blood
22	chr15:56207600-56209000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:56207600-56209200	Active TSS	Right Atrium	heart
24	chr15:56207600-56210000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:56207600-56210200	Flanking Active TSS	Osteobl	bone
26	chr15:56207600-56221200	Weak transcription	Right Ventricle	heart
27	chr15:56207800-56209000	Strong transcription	Primary T cells from cord blood	blood
28	chr15:56207800-56210600	Enhancers	HMEC	breast
29	chr15:56208000-56209600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr15:56208200-56210400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:56208400-56209000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr15:56208400-56209000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:56208400-56209000	Enhancers	Ovary	ovary
34	chr15:56208400-56209000	Active TSS	A549	lung
35	chr15:56208400-56209000	Flanking Active TSS	NHLF	lung
36	chr15:56208400-56209200	Active TSS	Brain Substantia Nigra	brain
37	chr15:56208400-56209200	Weak transcription	Fetal Kidney	kidney
38	chr15:56208400-56209400	Active TSS	Brain Anterior Caudate	brain
39	chr15:56208400-56209400	Flanking Active TSS	NHDF-Ad	bronchial
40	chr15:56208400-56210000	Flanking Active TSS	NH-A	brain
41	chr15:56208600-56209000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:56208600-56209000	Active TSS	Brain Cingulate Gyrus	brain
43	chr15:56208600-56209200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:56208600-56209200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr15:56208600-56209400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:56208600-56209400	Active TSS	Stomach Smooth Muscle	stomach
47	chr15:56208600-56209600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr15:56208600-56210400	Enhancers	Rectal Smooth Muscle	rectum
49	chr15:56208600-56218000	Weak transcription	Esophagus	oesophagus
50	chr15:56208800-56209000	Enhancers	Fetal Stomach	stomach

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