Variant report

Variant	rs12554047
Chromosome Location	chr9:6450183-6450184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12551361	0.96[EUR][1000 genomes]
rs12686562	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs407351	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs427077	0.89[EUR][1000 genomes]
rs4742205	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active 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	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS 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	21 gene(s)	inside rSNPs	diseases
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
2	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
3	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
4	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
5	chr9:6429200-6462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:6435000-6460400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:6435000-6463800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:6438000-6477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:6438600-6460000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:6441600-6454600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:6441600-6475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:6442200-6455800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:6443000-6461600	Weak transcription	HepG2	liver
15	chr9:6443600-6477600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:6443800-6450600	Weak transcription	Osteobl	bone
17	chr9:6444600-6450400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:6445000-6461200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr9:6445600-6451200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr9:6446200-6451400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr9:6446200-6460600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:6446400-6452200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:6446600-6451200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr9:6446600-6455200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:6446800-6452200	Weak transcription	Fetal Stomach	stomach
26	chr9:6446800-6463400	Weak transcription	Fetal Intestine Large	intestine
27	chr9:6446800-6468200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr9:6447000-6455200	Weak transcription	Fetal Intestine Small	intestine
29	chr9:6447200-6450800	Genic enhancers	HUVEC	blood vessel
30	chr9:6447200-6451000	Enhancers	Brain Anterior Caudate	brain
31	chr9:6447200-6451200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr9:6447200-6463400	Weak transcription	Lung	lung
33	chr9:6447400-6450600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:6447400-6450800	Enhancers	Brain Hippocampus Middle	brain
35	chr9:6447400-6451200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr9:6447400-6451400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr9:6447800-6450600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr9:6448200-6454000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:6448600-6451000	Genic enhancers	Primary T cells from cord blood	blood
40	chr9:6448800-6450400	Enhancers	Brain Angular Gyrus	brain
41	chr9:6448800-6450800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr9:6448800-6451000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:6448800-6451200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr9:6448800-6451200	Genic enhancers	Muscle Satellite Cultured Cells	--
45	chr9:6449000-6450200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:6449000-6450200	Enhancers	Duodenum Mucosa	Duodenum
47	chr9:6449000-6451000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:6449000-6451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr9:6449000-6451000	Enhancers	Brain Cingulate Gyrus	brain
50	chr9:6449000-6451000	Enhancers	Brain Substantia Nigra	brain

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