Variant report

Variant	rs12005522
Chromosome Location	chr9:110052660-110052661
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	chr9:110038034..110040721-chr9:110051893..110053905,2	MCF-7	breast:
2	chr9:110049612..110053509-chr9:110059334..110062914,3	K562	blood:

Extended variants
information (count: 31 )
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];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573652	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]
rs11573655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11573700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001235	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12001425	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004883	1.00[CHB][hapmap]
rs12005299	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16912372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17724694	0.93[EUR][1000 genomes]
rs56091145	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567660	0.84[EUR][1000 genomes]
rs62567661	0.84[EUR][1000 genomes]
rs62567691	0.84[EUR][1000 genomes]
rs62567693	0.84[EUR][1000 genomes]
rs62567694	0.84[EUR][1000 genomes]
rs62567696	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567704	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567738	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62569400	0.84[ASN][1000 genomes]
rs73668766	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73668780	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	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
6	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	chr9:110047200-110054600	Weak transcription	Lung	lung
2	chr9:110047600-110067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:110047800-110054200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr9:110048000-110053200	Weak transcription	Fetal Thymus	thymus
5	chr9:110048000-110056000	Weak transcription	Aorta	Aorta
6	chr9:110048000-110058400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:110048400-110052800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr9:110048400-110058000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr9:110048600-110058000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr9:110048800-110052800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr9:110048800-110055000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:110048800-110055200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:110048800-110055200	Weak transcription	HSMMtube	muscle
14	chr9:110048800-110056800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr9:110048800-110058600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr9:110048800-110059200	Enhancers	HepG2	liver
17	chr9:110048800-110061000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr9:110048800-110067800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:110048800-110069600	Weak transcription	Fetal Brain Male	brain
20	chr9:110049000-110052800	Enhancers	Primary T cells from cord blood	blood
21	chr9:110049000-110055000	Weak transcription	Fetal Brain Female	brain
22	chr9:110049000-110055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:110049000-110058800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:110049000-110061200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:110049000-110061400	Weak transcription	NH-A	brain
26	chr9:110049000-110063000	Enhancers	Liver	Liver
27	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:110049200-110054600	Weak transcription	NHEK	skin
30	chr9:110049200-110059200	Weak transcription	Fetal Intestine Small	intestine
31	chr9:110049200-110067000	Weak transcription	Fetal Muscle Leg	muscle
32	chr9:110049400-110067800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:110049800-110054000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr9:110049800-110058000	Weak transcription	Stomach Mucosa	stomach
35	chr9:110050000-110053400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:110050200-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:110050400-110052800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr9:110050400-110053400	Enhancers	Psoas Muscle	Psoas
39	chr9:110050400-110055000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:110050600-110052800	Enhancers	Brain Angular Gyrus	brain
41	chr9:110050600-110053600	Enhancers	Fetal Heart	heart
42	chr9:110050600-110054800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr9:110050800-110054000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr9:110051000-110053600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:110051000-110054600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:110051200-110052800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:110051200-110053200	Weak transcription	Osteobl	bone
48	chr9:110051200-110058400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:110051200-110066000	Weak transcription	Fetal Intestine Large	intestine
50	chr9:110051200-110067000	Weak transcription	Thymus	Thymus

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