Variant report

Variant	rs28609966
Chromosome Location	chr9:72049026-72049027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10114379	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10120658	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10123999	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10125502	1.00[AMR][1000 genomes]
rs11138569	0.91[AFR][1000 genomes]
rs11138764	0.85[AFR][1000 genomes]
rs12336955	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345295	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12347567	1.00[AFR][1000 genomes]
rs12351346	1.00[AFR][1000 genomes]
rs56386856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56951854	1.00[AMR][1000 genomes]
rs7022653	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647205	1.00[AMR][1000 genomes]
rs73647206	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647219	0.87[AFR][1000 genomes]
rs73647220	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647221	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv893432	chr9:72028323-72056397	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1047666	chr9:72028458-72049592	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	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
7	esv2761289	chr9:72028470-72049604	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1049763	chr9:72029588-72049592	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2422080	chr9:72029600-72049028	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1045274	chr9:72032381-72049592	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	esv3396573	chr9:72033229-72054457	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv2761532	chr9:72035189-72049604	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv442554	chr9:72035193-72049028	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1038185	chr9:72035199-72057304	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	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
19	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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72036600-72082600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72037200-72055600	Weak transcription	Fetal Lung	lung
3	chr9:72037200-72056200	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:72040800-72057400	Weak transcription	Fetal Heart	heart
5	chr9:72041200-72069600	Weak transcription	Gastric	stomach
6	chr9:72041600-72049400	Strong transcription	Liver	Liver
7	chr9:72042000-72070400	Weak transcription	Spleen	Spleen
8	chr9:72042800-72063800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:72043200-72063800	Weak transcription	Brain Substantia Nigra	brain
10	chr9:72043400-72055400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:72043400-72055600	Weak transcription	Brain Angular Gyrus	brain
12	chr9:72044200-72084400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:72045000-72084400	Weak transcription	Fetal Intestine Large	intestine
14	chr9:72045400-72050600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:72045800-72064200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:72046000-72056400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:72046400-72085600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:72046600-72049400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:72046800-72055600	Weak transcription	Brain Germinal Matrix	brain
20	chr9:72047000-72055600	Weak transcription	Adipose Nuclei	Adipose
21	chr9:72047000-72055600	Weak transcription	Pancreas	Pancrea
22	chr9:72047000-72055600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:72047000-72056600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:72047000-72056800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:72047000-72081800	Weak transcription	Fetal Kidney	kidney
26	chr9:72047200-72055600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:72047400-72055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:72047600-72049200	Enhancers	NHEK	skin
29	chr9:72047800-72049200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:72047800-72049200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:72047800-72055400	Weak transcription	Aorta	Aorta
32	chr9:72047800-72055600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:72048000-72049200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:72048000-72049200	Enhancers	HMEC	breast
35	chr9:72048000-72055600	Weak transcription	Brain Anterior Caudate	brain
36	chr9:72048000-72068600	Weak transcription	Left Ventricle	heart
37	chr9:72048200-72049200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:72048200-72049200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:72048200-72049200	Enhancers	NHDF-Ad	bronchial
40	chr9:72048200-72055400	Weak transcription	Fetal Brain Female	brain
41	chr9:72048200-72055400	Weak transcription	Fetal Stomach	stomach
42	chr9:72048400-72049200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:72048400-72055400	Weak transcription	Ovary	ovary
44	chr9:72048400-72055800	Weak transcription	Brain Hippocampus Middle	brain
45	chr9:72048600-72055400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:72049000-72049200	Enhancers	Lung	lung
47	chr9:72049000-72055600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:72049000-72059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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