Variant report

Variant	rs906811
Chromosome Location	chr15:56229547-56229548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56229297..56231144-chr15:56284822..56287576,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069869	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10518823	0.91[EUR][1000 genomes]
rs12439899	0.83[EUR][1000 genomes]
rs12898478	0.91[EUR][1000 genomes]
rs12899701	1.00[CEU][hapmap]
rs12901802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12902173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12904236	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12908286	0.81[EUR][1000 genomes]
rs12911101	0.81[EUR][1000 genomes]
rs17819270	0.93[EUR][1000 genomes]
rs1912397	0.91[EUR][1000 genomes]
rs1912403	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2899593	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs34162982	1.00[EUR][1000 genomes]
rs34223710	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34333169	0.81[EUR][1000 genomes]
rs34652186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34718758	0.82[EUR][1000 genomes]
rs34727807	0.91[EUR][1000 genomes]
rs34995202	0.91[EUR][1000 genomes]
rs35086304	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35142499	0.96[EUR][1000 genomes]
rs35313340	0.81[EUR][1000 genomes]
rs35485562	0.83[EUR][1000 genomes]
rs4296197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66473405	0.83[EUR][1000 genomes]
rs66857236	0.91[EUR][1000 genomes]
rs67046147	0.93[EUR][1000 genomes]
rs67825863	0.91[EUR][1000 genomes]
rs71476753	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476755	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476760	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476766	0.83[EUR][1000 genomes]
rs7172454	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7182037	0.83[EUR][1000 genomes]
rs8038204	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039617	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8043427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs906811	CYP19A1	cis	cerebellum	SCAN
rs906811	UNC13C	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56201000-56230000	Weak transcription	Fetal Intestine Large	intestine
2	chr15:56208800-56230000	Weak transcription	Liver	Liver
3	chr15:56209000-56230400	Weak transcription	Primary T cells from cord blood	blood
4	chr15:56209200-56230200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:56209200-56230200	Weak transcription	Aorta	Aorta
6	chr15:56209600-56230800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:56209600-56247400	Weak transcription	Psoas Muscle	Psoas
8	chr15:56210200-56229600	Weak transcription	HSMMtube	muscle
9	chr15:56210200-56229800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:56211400-56230800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:56211800-56242400	Weak transcription	Hela-S3	cervix
12	chr15:56216800-56230000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:56217200-56230000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:56218800-56230200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:56219200-56230200	Weak transcription	Fetal Intestine Small	intestine
16	chr15:56221600-56242400	Weak transcription	NHEK	skin
17	chr15:56221800-56230200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:56222200-56234200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:56224000-56230000	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:56226200-56245800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:56227400-56230600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:56228200-56230000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:56228600-56230600	Weak transcription	Fetal Lung	lung
24	chr15:56228800-56229800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:56228800-56229800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:56228800-56234600	Weak transcription	Placenta	Placenta
27	chr15:56229000-56231400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:56229200-56229600	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr15:56229200-56229600	Enhancers	K562	blood
30	chr15:56229200-56229800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr15:56229200-56229800	Enhancers	HUVEC	blood vessel
32	chr15:56229200-56230000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:56229200-56230000	Enhancers	Fetal Kidney	kidney
34	chr15:56229200-56230200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:56229400-56229600	Enhancers	HSMM	muscle
36	chr15:56229400-56229600	Enhancers	NHLF	lung
37	chr15:56229400-56229800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:56229400-56230000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:56229400-56230800	ZNF genes & repeats	A549	lung
40	chr15:56229400-56234600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:56229400-56259000	Weak transcription	Ovary	ovary
42	chr15:56229400-56259400	Weak transcription	Small Intestine	intestine

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