Variant report

Variant	rs13288779
Chromosome Location	chr9:8522483-8522484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13301979	0.85[CHD][hapmap]
rs1535678	0.80[ASN][1000 genomes]
rs1538192	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs16928072	0.80[CHB][hapmap]
rs2184978	0.82[GIH][hapmap]
rs35789317	0.82[ASN][1000 genomes]
rs6477314	0.80[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13288779	JAK2	cis	parietal	SCAN
rs13288779	C9orf68	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
2	chr9:8483800-8524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:8486200-8522800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:8486200-8523200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
6	chr9:8492400-8528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:8493200-8523200	Weak transcription	Fetal Stomach	stomach
8	chr9:8493200-8531200	Weak transcription	Fetal Brain Female	brain
9	chr9:8494200-8531200	Weak transcription	Fetal Brain Male	brain
10	chr9:8509400-8528600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:8509800-8532800	Weak transcription	Brain Angular Gyrus	brain
12	chr9:8513200-8523000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:8517000-8523600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr9:8518000-8528600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:8518200-8526400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:8518400-8526000	Weak transcription	Ovary	ovary
17	chr9:8518400-8533800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:8518400-8534000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:8518400-8555200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:8519800-8531600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:8520000-8524000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:8520000-8531200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:8520400-8522600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:8521200-8525000	Strong transcription	Fetal Lung	lung
25	chr9:8521600-8523400	Enhancers	Brain Substantia Nigra	brain
26	chr9:8521800-8526200	Weak transcription	Dnd41	blood
27	chr9:8522000-8523800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:8522000-8528200	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:8522000-8528600	Weak transcription	Brain Germinal Matrix	brain
30	chr9:8522200-8531400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:8522400-8524000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:8522400-8529200	Weak transcription	Brain Anterior Caudate	brain
33	chr9:8522400-8530800	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:8522400-8531600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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