Variant report

Variant	rs10962484
Chromosome Location	chr9:16550670-16550671
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:16550024..16551022-chrX:41301770..41302313,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10116857	0.84[EUR][1000 genomes]
rs10118895	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10120002	0.82[ASW][hapmap];0.80[EUR][1000 genomes]
rs10120281	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10122372	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10123515	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10124530	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10125014	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs10738437	0.89[GIH][hapmap]
rs10738440	1.00[CEU][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs10756764	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10756765	0.94[GIH][hapmap];0.92[TSI][hapmap]
rs10962510	0.90[EUR][1000 genomes]
rs12000426	1.00[CEU][hapmap]
rs12004304	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12337676	0.80[AMR][1000 genomes]
rs12339625	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12340504	0.86[EUR][1000 genomes]
rs12350242	0.84[EUR][1000 genomes]
rs1337393	0.80[AMR][1000 genomes]
rs1415475	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1415476	0.82[MEX][hapmap]
rs1538102	0.83[EUR][1000 genomes]
rs16934816	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16934842	0.84[EUR][1000 genomes]
rs16934855	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16934875	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs16934886	0.83[EUR][1000 genomes]
rs17738890	0.97[EUR][1000 genomes]
rs2095657	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2149159	0.82[EUR][1000 genomes]
rs28428651	1.00[EUR][1000 genomes]
rs28457730	0.91[EUR][1000 genomes]
rs28490464	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28501274	0.90[EUR][1000 genomes]
rs28648047	1.00[EUR][1000 genomes]
rs28651010	0.93[EUR][1000 genomes]
rs4466493	0.83[EUR][1000 genomes]
rs4961725	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs56218971	0.97[EUR][1000 genomes]
rs59379949	0.88[EUR][1000 genomes]
rs7018743	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7018877	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7019016	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7019105	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7019625	0.86[EUR][1000 genomes]
rs7032239	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7032523	1.00[CEU][hapmap]
rs7032772	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7036282	0.86[EUR][1000 genomes]
rs7048805	1.00[EUR][1000 genomes]
rs725011	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73417477	1.00[EUR][1000 genomes]
rs7470623	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7854979	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7859395	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7859971	0.91[EUR][1000 genomes]
rs7862214	0.80[EUR][1000 genomes]
rs7870380	0.81[EUR][1000 genomes]
rs7870508	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7870730	0.83[EUR][1000 genomes]
rs7873338	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16525000-16551400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:16528000-16553200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:16528800-16551200	Weak transcription	Fetal Intestine Large	intestine
4	chr9:16531400-16551200	Weak transcription	Fetal Stomach	stomach
5	chr9:16536000-16552200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:16536200-16551600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:16541200-16552000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:16541400-16551200	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:16542000-16551200	Weak transcription	Adipose Nuclei	Adipose
10	chr9:16542600-16550800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:16542600-16551200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:16542600-16564000	Weak transcription	HUVEC	blood vessel
13	chr9:16542800-16551000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:16542800-16551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:16542800-16554800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:16543800-16554600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:16543800-16567000	Weak transcription	HSMMtube	muscle
18	chr9:16544000-16551000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:16544000-16559600	Weak transcription	Small Intestine	intestine
20	chr9:16545000-16554000	Weak transcription	Fetal Kidney	kidney
21	chr9:16545600-16552400	Weak transcription	Aorta	Aorta
22	chr9:16545800-16551800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:16545800-16552000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:16546000-16554600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:16546000-16559600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:16546000-16559800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:16546000-16568400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:16546200-16550800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:16546400-16551200	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:16546800-16551000	Weak transcription	Ovary	ovary
31	chr9:16546800-16552800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:16547400-16550800	Weak transcription	Fetal Lung	lung
33	chr9:16548200-16550800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:16548200-16550800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:16548200-16551000	Weak transcription	NH-A	brain
36	chr9:16548200-16551400	Weak transcription	NHLF	lung
37	chr9:16548200-16552400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:16548400-16550800	Weak transcription	Osteobl	bone
39	chr9:16550000-16556400	Weak transcription	Fetal Intestine Small	intestine
40	chr9:16550200-16554000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:16550400-16552800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:16550600-16551800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:16550600-16552600	Strong transcription	HSMM	muscle
44	chr9:16550600-16552800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:16550600-16552800	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr9:16550600-16552800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr9:16550600-16553400	Strong transcription	NHDF-Ad	bronchial

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