Variant report

Variant	rs12336955
Chromosome Location	chr9:72066686-72066687
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	chr9:72059861..72061593-chr9:72066565..72068301,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10114379	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10120658	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10123999	1.00[AMR][1000 genomes]
rs10125502	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11138569	0.83[AFR][1000 genomes]
rs11138764	0.97[AFR][1000 genomes]
rs12345295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12346368	0.81[AFR][1000 genomes]
rs12347567	0.88[AFR][1000 genomes]
rs12351346	0.88[AFR][1000 genomes]
rs28609966	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56386856	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56951854	1.00[AMR][1000 genomes]
rs7022653	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647205	1.00[AMR][1000 genomes]
rs73647206	1.00[AMR][1000 genomes]
rs73647220	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1048256	chr9:72032381-72067786	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1045239	chr9:72032381-72067942	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1041436	chr9:72032381-72069314	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1052872	chr9:72040184-72081554	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1037109	chr9:72040184-72120270	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1039966	chr9:72057304-72181564	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72036600-72082600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72041200-72069600	Weak transcription	Gastric	stomach
3	chr9:72042000-72070400	Weak transcription	Spleen	Spleen
4	chr9:72044200-72084400	Weak transcription	Fetal Intestine Small	intestine
5	chr9:72045000-72084400	Weak transcription	Fetal Intestine Large	intestine
6	chr9:72046400-72085600	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:72047000-72081800	Weak transcription	Fetal Kidney	kidney
8	chr9:72048000-72068600	Weak transcription	Left Ventricle	heart
9	chr9:72054000-72073200	Weak transcription	Right Ventricle	heart
10	chr9:72055200-72073000	Strong transcription	Liver	Liver
11	chr9:72056000-72082600	Weak transcription	Pancreas	Pancrea
12	chr9:72056400-72080800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:72058200-72080200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:72058400-72070600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:72059400-72066800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:72059400-72067000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:72059400-72072400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:72059400-72080200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:72059600-72069600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:72061000-72070000	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr9:72061200-72071400	Strong transcription	Brain Germinal Matrix	brain
22	chr9:72061800-72067000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:72062200-72068800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:72062200-72070200	Strong transcription	Fetal Stomach	stomach
25	chr9:72062200-72072600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:72062800-72072400	Strong transcription	Ovary	ovary
27	chr9:72063600-72067000	Strong transcription	Brain Anterior Caudate	brain
28	chr9:72063600-72067400	Strong transcription	Fetal Muscle Leg	muscle
29	chr9:72063800-72067400	Strong transcription	Aorta	Aorta
30	chr9:72063800-72070000	Strong transcription	Brain Substantia Nigra	brain
31	chr9:72064600-72068600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:72064600-72084200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:72064600-72084200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:72064800-72067400	Weak transcription	Fetal Lung	lung
35	chr9:72064800-72069400	Weak transcription	Adipose Nuclei	Adipose
36	chr9:72064800-72071400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:72064800-72083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:72065600-72066800	Strong transcription	Fetal Brain Male	brain
39	chr9:72065600-72068200	Weak transcription	Primary T cells from cord blood	blood
40	chr9:72065600-72068800	Strong transcription	Brain Angular Gyrus	brain
41	chr9:72065800-72067400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr9:72065800-72071400	Strong transcription	Fetal Brain Female	brain
43	chr9:72066000-72066800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr9:72066000-72067400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr9:72066000-72070000	Strong transcription	Brain Hippocampus Middle	brain
46	chr9:72066200-72071400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:72066200-72081000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:72066400-72067800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr9:72066400-72075400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:72066600-72068400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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