Variant report

Variant	rs1260132
Chromosome Location	chr9:5789939-5789940
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5784098..5787318-chr9:5787843..5791825,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10975340	1.00[EUR][1000 genomes]
rs1141025	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1260128	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1260130	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260134	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1260135	1.00[EUR][1000 genomes]
rs1745887	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1745888	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1776008	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2476262	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760408	1.00[EUR][1000 genomes]
rs2760409	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760410	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2797512	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2797514	1.00[EUR][1000 genomes]
rs2797516	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2797517	0.89[AFR][1000 genomes]
rs2797519	1.00[EUR][1000 genomes]
rs58370080	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6477001	1.00[EUR][1000 genomes]
rs6477002	1.00[EUR][1000 genomes]
rs7037680	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7042100	1.00[EUR][1000 genomes]
rs7046793	1.00[EUR][1000 genomes]
rs73377834	1.00[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	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019444	chr9:5598677-5807009	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv892151	chr9:5602528-5841438	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5775000-5797000	Weak transcription	Psoas Muscle	Psoas
2	chr9:5779000-5792800	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr9:5779000-5793000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr9:5779200-5790800	Strong transcription	Primary T cells from cord blood	blood
5	chr9:5779200-5792800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:5779200-5809600	Weak transcription	NHDF-Ad	bronchial
7	chr9:5779200-5832200	Weak transcription	Fetal Brain Male	brain
8	chr9:5779600-5814000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:5779600-5827800	Weak transcription	Small Intestine	intestine
10	chr9:5780400-5793200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:5780400-5794200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:5780600-5792000	Weak transcription	Right Ventricle	heart
13	chr9:5780600-5799400	Weak transcription	Osteobl	bone
14	chr9:5780800-5790200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:5780800-5791200	Weak transcription	HSMMtube	muscle
16	chr9:5781000-5799400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:5781800-5790200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:5782000-5793000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:5783400-5790000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:5783800-5791000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:5784200-5831600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:5785400-5792200	Strong transcription	Primary B cells from cord blood	blood
23	chr9:5786800-5832200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:5787000-5790200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:5787000-5791200	Weak transcription	Right Atrium	heart
26	chr9:5787000-5791800	Weak transcription	Brain Germinal Matrix	brain
27	chr9:5787000-5830200	Weak transcription	Dnd41	blood
28	chr9:5787200-5791000	Weak transcription	Fetal Heart	heart
29	chr9:5787200-5791200	Weak transcription	Brain Substantia Nigra	brain
30	chr9:5787200-5791200	Weak transcription	NHLF	lung
31	chr9:5787200-5793000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr9:5787200-5799200	Weak transcription	Fetal Kidney	kidney
33	chr9:5787200-5799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:5787200-5799400	Weak transcription	Fetal Lung	lung
35	chr9:5787200-5799400	Weak transcription	Placenta	Placenta
36	chr9:5787200-5804200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:5787200-5815000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:5787400-5790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:5787400-5790800	Weak transcription	Spleen	Spleen
40	chr9:5787400-5791000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:5787400-5791200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:5787400-5791200	Weak transcription	Brain Angular Gyrus	brain
43	chr9:5787400-5791400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:5787400-5792600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:5787400-5793200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr9:5787400-5793600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:5787400-5796400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr9:5787400-5797600	Weak transcription	A549	lung
49	chr9:5787400-5799000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:5787400-5799400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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