Variant report

Variant	rs12553563
Chromosome Location	chr9:8382108-8382109
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10435748	0.84[ASN][1000 genomes]
rs10815844	0.80[JPT][hapmap]
rs10815851	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10815852	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10815872	1.00[CEU][hapmap]
rs10977017	0.95[JPT][hapmap]
rs10977018	1.00[JPT][hapmap]
rs10977019	1.00[JPT][hapmap]
rs10977020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10977026	1.00[YRI][hapmap]
rs10977027	0.84[ASN][1000 genomes]
rs10977047	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10977048	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10977049	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10977050	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10977058	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10977088	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs1156793	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1156794	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12352188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13291309	1.00[YRI][hapmap]
rs1392520	0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs1392521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1392522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1392524	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1500324	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1500328	0.95[JPT][hapmap]
rs16927841	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1875239	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1909755	0.85[JPT][hapmap]
rs2221184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291958	0.81[JPT][hapmap]
rs3739577	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs3847293	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4742498	0.94[CHB][hapmap]
rs7030727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031533	0.81[JPT][hapmap]
rs7854520	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs989814	0.81[JPT][hapmap]
rs991250	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:8364600-8382200	Weak transcription	Ovary	ovary
4	chr9:8364800-8401600	Weak transcription	Brain Germinal Matrix	brain
5	chr9:8365000-8395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:8365200-8386800	Weak transcription	Brain Anterior Caudate	brain
7	chr9:8365600-8386200	Weak transcription	Brain Angular Gyrus	brain
8	chr9:8365600-8386200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:8366800-8383000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:8367200-8394600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:8367200-8399800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:8373000-8402200	Weak transcription	Fetal Kidney	kidney
13	chr9:8373600-8385800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:8374000-8394400	Weak transcription	Fetal Heart	heart
15	chr9:8374200-8382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:8374600-8386800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:8376600-8386800	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:8376800-8386600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:8376800-8393200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:8376800-8401800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:8377800-8383400	Weak transcription	Fetal Brain Male	brain
22	chr9:8377800-8406400	Weak transcription	Fetal Brain Female	brain
23	chr9:8380600-8382200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:8381800-8382600	Enhancers	Fetal Intestine Large	intestine
25	chr9:8381800-8383400	Enhancers	Pancreas	Pancrea
26	chr9:8381800-8383600	Enhancers	Aorta	Aorta
27	chr9:8382000-8382600	Enhancers	Gastric	stomach
28	chr9:8382000-8383800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:8382000-8384400	Enhancers	Fetal Lung	lung

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