Variant report

Variant	rs12552422
Chromosome Location	chr9:8853008-8853009
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12552174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570305	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2570965	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2814717	0.91[CHB][hapmap]
rs2814718	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2814719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7466280	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs767209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12552422	RP11-75C9.1	cis	Artery Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8843000-8855200	Weak transcription	Fetal Stomach	stomach
2	chr9:8843000-8856600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:8843200-8854200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:8844000-8854400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:8845800-8855600	Weak transcription	Ovary	ovary
6	chr9:8845800-8856600	Weak transcription	Psoas Muscle	Psoas
7	chr9:8847000-8854600	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:8850000-8853600	Enhancers	Brain Cingulate Gyrus	brain
9	chr9:8850800-8854600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:8850800-8854600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:8851000-8853400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr9:8851200-8856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:8851800-8854200	Enhancers	Brain Anterior Caudate	brain
14	chr9:8852000-8853600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:8852000-8854600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:8852200-8855800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:8852400-8853200	Active TSS	Brain Hippocampus Middle	brain
18	chr9:8852600-8853200	Flanking Active TSS	Fetal Brain Female	brain
19	chr9:8852600-8853600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:8852600-8854000	Enhancers	Brain Substantia Nigra	brain
21	chr9:8852600-8854200	Bivalent Enhancer	Fetal Lung	lung
22	chr9:8852600-8854800	Weak transcription	Liver	Liver
23	chr9:8852600-8855600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:8852800-8853200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:8852800-8853400	Enhancers	Fetal Brain Male	brain
26	chr9:8852800-8853600	Weak transcription	Fetal Heart	heart
27	chr9:8852800-8853800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:8852800-8854000	Enhancers	Brain Angular Gyrus	brain
29	chr9:8852800-8854200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:8852800-8854200	Enhancers	Brain Germinal Matrix	brain
31	chr9:8852800-8854400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr9:8852800-8855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:8852800-8855200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:8853000-8853600	Weak transcription	Fetal Kidney	kidney
35	chr9:8853000-8854000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:8853000-8854400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:8853000-8854600	Weak transcription	Aorta	Aorta
38	chr9:8853000-8854800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:8853000-8856400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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