Variant report

Variant	rs11999333
Chromosome Location	chr9:102896621-102896622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102890729..102892590-chr9:102896072..102898003,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11998846	1.00[AMR][1000 genomes]
rs11999065	1.00[AMR][1000 genomes]
rs11999405	1.00[AMR][1000 genomes]
rs11999759	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11999920	1.00[AMR][1000 genomes]
rs12000423	1.00[AMR][1000 genomes]
rs12000833	1.00[AMR][1000 genomes]
rs12001165	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12001197	1.00[AMR][1000 genomes]
rs12001218	1.00[AMR][1000 genomes]
rs12001575	1.00[AMR][1000 genomes]
rs12003270	1.00[AMR][1000 genomes]
rs12003337	1.00[AMR][1000 genomes]
rs12003593	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12004561	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12005084	1.00[AMR][1000 genomes]
rs12005328	1.00[AMR][1000 genomes]
rs12005758	1.00[AMR][1000 genomes]
rs28704948	1.00[AMR][1000 genomes]
rs58604350	1.00[AMR][1000 genomes]
rs59127855	1.00[AMR][1000 genomes]
rs61163672	1.00[AMR][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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102862200-102902400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:102867000-102899800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:102869200-102901800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:102869400-102899000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:102870000-102902200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:102871200-102897400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:102873800-102900200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:102874200-102897600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:102874200-102898800	Weak transcription	Fetal Brain Male	brain
10	chr9:102874200-102902600	Weak transcription	HMEC	breast
11	chr9:102874200-102902600	Weak transcription	NHEK	skin
12	chr9:102874200-102912600	Weak transcription	Osteobl	bone
13	chr9:102874200-102937600	Weak transcription	Aorta	Aorta
14	chr9:102874600-102897800	Weak transcription	Brain Germinal Matrix	brain
15	chr9:102879800-102935000	Weak transcription	Ovary	ovary
16	chr9:102880000-102897600	Weak transcription	Adipose Nuclei	Adipose
17	chr9:102881400-102902200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:102882000-102899000	Weak transcription	Psoas Muscle	Psoas
19	chr9:102883000-102937600	Weak transcription	Fetal Intestine Large	intestine
20	chr9:102883800-102928400	Weak transcription	Primary T cells from cord blood	blood
21	chr9:102884400-102901800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:102884800-102898400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:102885200-102932600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:102885600-102897600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:102885600-102900400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr9:102886000-102898400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:102886000-102899600	Weak transcription	GM12878-XiMat	blood
28	chr9:102886000-102931600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:102887000-102901800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:102887800-102903400	Weak transcription	Pancreas	Pancrea
31	chr9:102887800-102922200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:102888000-102902600	Weak transcription	HepG2	liver
33	chr9:102888200-102897000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:102888600-102896800	Weak transcription	Stomach Mucosa	stomach
35	chr9:102889000-102902000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:102889000-102907000	Weak transcription	K562	blood
37	chr9:102889200-102901600	Weak transcription	Hela-S3	cervix
38	chr9:102889200-102936000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:102889400-102897600	Weak transcription	Brain Angular Gyrus	brain
40	chr9:102889400-102898800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:102889600-102934600	Weak transcription	Fetal Intestine Small	intestine
42	chr9:102890800-102896800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:102890800-102896800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr9:102891000-102904600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:102891200-102899800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:102891800-102935200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:102892200-102900600	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:102892200-102909200	Weak transcription	Fetal Stomach	stomach
49	chr9:102892600-102897000	Weak transcription	HSMM	muscle
50	chr9:102892600-102898800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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