Variant report

Variant	rs12003277
Chromosome Location	chr9:16575774-16575775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12004947	0.83[AFR][1000 genomes]
rs16934813	0.89[YRI][hapmap];0.94[AFR][1000 genomes]
rs16934814	0.90[YRI][hapmap]
rs57946399	0.96[AFR][1000 genomes]
rs60445897	0.97[AFR][1000 genomes]
rs6475064	0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6475065	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7018594	0.86[YRI][hapmap]
rs7029578	0.84[YRI][hapmap]
rs7029648	0.86[YRI][hapmap]
rs73417482	0.87[AFR][1000 genomes]
rs73417498	0.91[AFR][1000 genomes]
rs73417499	0.91[AFR][1000 genomes]
rs73419408	0.96[AFR][1000 genomes]
rs73419411	0.96[AFR][1000 genomes]
rs73419419	0.94[AFR][1000 genomes]
rs73419428	0.97[AFR][1000 genomes]
rs73419430	0.86[AFR][1000 genomes]
rs73419435	0.91[AFR][1000 genomes]
rs73419478	0.89[AFR][1000 genomes]
rs7847768	0.81[YRI][hapmap]
rs7858087	0.91[AFR][1000 genomes]
rs7861455	0.91[AFR][1000 genomes]
rs943746	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs943747	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs943748	0.86[YRI][hapmap];0.81[AFR][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	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
5	nsv528443	chr9:16570142-16581967	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16569800-16582400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:16570800-16575800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr9:16571400-16582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:16572000-16581800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:16572800-16575800	Weak transcription	NHDF-Ad	bronchial
6	chr9:16572800-16581400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:16572800-16581800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:16572800-16582600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:16573000-16575800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:16573200-16586400	Weak transcription	Pancreas	Pancrea
11	chr9:16573200-16591800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:16574600-16580000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:16574800-16576400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr9:16574800-16576400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr9:16574800-16576600	Enhancers	Fetal Stomach	stomach
16	chr9:16575000-16576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:16575000-16576200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr9:16575000-16576600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr9:16575200-16575800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:16575200-16575800	Enhancers	Placenta	Placenta
21	chr9:16575200-16576000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:16575200-16576000	Enhancers	Ovary	ovary
23	chr9:16575200-16576000	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:16575200-16576000	Enhancers	NHLF	lung
25	chr9:16575200-16576200	Enhancers	Fetal Kidney	kidney
26	chr9:16575200-16576400	Enhancers	A549	lung
27	chr9:16575200-16578800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:16575400-16575800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:16575400-16575800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr9:16575400-16575800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:16575400-16575800	Enhancers	HSMMtube	muscle
32	chr9:16575400-16576000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr9:16575400-16576200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr9:16575400-16576400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:16575400-16582400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:16575600-16575800	Enhancers	Colonic Mucosa	Colon
37	chr9:16575600-16575800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr9:16575600-16575800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr9:16575600-16575800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr9:16575600-16575800	Enhancers	Osteobl	bone
41	chr9:16575600-16576000	Enhancers	H9 Cell Line	embryonic stem cell
42	chr9:16575600-16576000	Enhancers	Adipose Nuclei	Adipose
43	chr9:16575600-16576000	Enhancers	HSMM	muscle
44	chr9:16575600-16576200	Enhancers	Fetal Muscle Leg	muscle
45	chr9:16575600-16576200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr9:16575600-16576200	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr9:16575600-16576400	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr9:16575600-16576400	Enhancers	Fetal Lung	lung
49	chr9:16575600-16576600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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