Variant report

Variant	rs11573652
Chromosome Location	chr9:110058263-110058264
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110044182..110049393-chr9:110054071..110058486,10	MCF-7	breast:
2	chr9:110056937..110059349-chr9:110068583..110071542,3	MCF-7	breast:
3	chr9:110058012..110060076-chr9:110062055..110063823,2	MCF-7	breast:
4	chr9:110052754..110054534-chr9:110055786..110058633,2	K562	blood:
5	chr9:110056091..110058326-chr9:110068652..110070391,2	K562	blood:
6	chr9:110050921..110052628-chr9:110056459..110059114,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10978789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11573700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12001425	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004883	1.00[CHB][hapmap]
rs12005299	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12005522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16912372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17724694	0.97[EUR][1000 genomes]
rs56091145	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567660	0.87[EUR][1000 genomes]
rs62567661	0.87[EUR][1000 genomes]
rs62567691	0.87[EUR][1000 genomes]
rs62567693	0.87[EUR][1000 genomes]
rs62567694	0.87[EUR][1000 genomes]
rs62567696	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567704	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567738	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62569400	0.84[ASN][1000 genomes]
rs73668766	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73668780	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110047600-110067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:110048000-110058400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:110048800-110058600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr9:110048800-110059200	Enhancers	HepG2	liver
5	chr9:110048800-110061000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr9:110048800-110067800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:110048800-110069600	Weak transcription	Fetal Brain Male	brain
8	chr9:110049000-110058800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:110049000-110061200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:110049000-110061400	Weak transcription	NH-A	brain
11	chr9:110049000-110063000	Enhancers	Liver	Liver
12	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:110049200-110059200	Weak transcription	Fetal Intestine Small	intestine
15	chr9:110049200-110067000	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:110049400-110067800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:110050200-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:110051200-110058400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:110051200-110066000	Weak transcription	Fetal Intestine Large	intestine
20	chr9:110051200-110067000	Weak transcription	Thymus	Thymus
21	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:110052000-110066800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr9:110052200-110061200	Weak transcription	Dnd41	blood
24	chr9:110052600-110063200	Weak transcription	Placenta	Placenta
25	chr9:110052600-110067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:110052600-110067000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:110052600-110068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:110052600-110068600	Weak transcription	Brain Germinal Matrix	brain
29	chr9:110052600-110068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:110052600-110069200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:110052800-110061200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:110052800-110066000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:110053400-110068600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:110053600-110061200	Weak transcription	Hela-S3	cervix
35	chr9:110053600-110063200	Weak transcription	Fetal Thymus	thymus
36	chr9:110053600-110063400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:110054600-110058400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:110054600-110058600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr9:110055200-110058400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:110055200-110058400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr9:110055200-110058400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:110055400-110058800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr9:110055600-110058800	Enhancers	A549	lung
44	chr9:110055600-110061200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr9:110055600-110063000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr9:110055600-110067600	Weak transcription	HSMMtube	muscle
47	chr9:110055600-110068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr9:110055800-110061200	Weak transcription	HMEC	breast
49	chr9:110055800-110068600	Weak transcription	Fetal Brain Female	brain
50	chr9:110055800-110068600	Weak transcription	Placenta Amnion	Placenta Amnion

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