Variant report

Variant	rs11788588
Chromosome Location	chr9:19065612-19065613
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	chr9:19057659..19060410-chr9:19065163..19067075,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11787990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11788085	0.86[EUR][1000 genomes]
rs11788977	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11789049	0.81[EUR][1000 genomes]
rs11789469	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11790182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11791226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11791674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11791698	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11792293	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11792398	0.81[EUR][1000 genomes]
rs11793228	1.00[AMR][1000 genomes]
rs11793687	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11795205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11795374	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16937266	0.81[EUR][1000 genomes]
rs16937284	0.86[EUR][1000 genomes]
rs17236531	0.86[EUR][1000 genomes]
rs2229536	1.00[AMR][1000 genomes]
rs34387057	0.81[EUR][1000 genomes]
rs35004770	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35568725	1.00[AMR][1000 genomes]
rs41269003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41269015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41303687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41316035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56310265	1.00[AMR][1000 genomes]
rs62560426	0.81[EUR][1000 genomes]
rs62560427	0.83[EUR][1000 genomes]
rs62560428	0.81[EUR][1000 genomes]
rs62560429	0.81[EUR][1000 genomes]
rs62560431	0.83[EUR][1000 genomes]
rs62563562	0.86[EUR][1000 genomes]
rs67330394	1.00[AMR][1000 genomes]
rs67844957	0.81[EUR][1000 genomes]
rs72696432	0.90[EUR][1000 genomes]
rs72696433	0.86[EUR][1000 genomes]
rs72696445	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72696446	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72696447	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72696449	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72696450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696462	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696463	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696469	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696470	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72696479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72696488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696491	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72696499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72696500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72696501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72696502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72698303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72698305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72698306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72698310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72698311	1.00[AMR][1000 genomes]
rs72698312	1.00[AMR][1000 genomes]
rs72698318	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	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:19050800-19074200	Weak transcription	Lung	lung
3	chr9:19051400-19066400	Weak transcription	Colonic Mucosa	Colon
4	chr9:19051600-19074400	Weak transcription	Spleen	Spleen
5	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:19051800-19070200	Weak transcription	Fetal Kidney	kidney
7	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:19052000-19075200	Weak transcription	Right Ventricle	heart
9	chr9:19052400-19077000	Weak transcription	Pancreas	Pancrea
10	chr9:19052800-19074400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:19052800-19075600	Weak transcription	Aorta	Aorta
12	chr9:19052800-19092400	Weak transcription	Fetal Brain Male	brain
13	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:19055000-19072600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:19055600-19082600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr9:19055800-19079800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:19055800-19085200	Strong transcription	Liver	Liver
21	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:19056000-19086000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:19056400-19073600	Strong transcription	Hela-S3	cervix
28	chr9:19056600-19066600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:19056600-19067200	Strong transcription	Fetal Thymus	thymus
30	chr9:19056600-19067800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr9:19056600-19070800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:19056600-19071600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:19056600-19072400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:19056600-19074600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:19056600-19094800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:19056600-19095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:19056600-19095400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:19056600-19096000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr9:19056800-19071400	Strong transcription	Primary T cells from cord blood	blood
40	chr9:19056800-19083000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr9:19056800-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:19057000-19067400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:19057000-19074000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:19057200-19078200	Strong transcription	Primary B cells from cord blood	blood
45	chr9:19057400-19075800	Weak transcription	Gastric	stomach
46	chr9:19057600-19066400	Weak transcription	Fetal Heart	heart
47	chr9:19057600-19077000	Weak transcription	Esophagus	oesophagus
48	chr9:19059200-19067000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:19059200-19074400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:19059800-19069000	Weak transcription	Placenta Amnion	Placenta Amnion

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