Variant report

Variant	rs3818346
Chromosome Location	chr9:8521244-8521245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2031212	0.83[JPT][hapmap]
rs2184978	0.88[ASW][hapmap]
rs62534049	0.86[EUR][1000 genomes]
rs6477314	0.82[MKK][hapmap];0.86[AMR][1000 genomes]
rs7023008	1.00[ASW][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7024591	0.89[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039690	0.94[ASW][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][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	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	nsv892226	chr9:8435525-8522326	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
2	chr9:8442200-8522200	Weak transcription	Liver	Liver
3	chr9:8483800-8524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:8486000-8522200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:8486200-8522800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:8486200-8523200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
8	chr9:8492400-8528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:8493200-8523200	Weak transcription	Fetal Stomach	stomach
10	chr9:8493200-8531200	Weak transcription	Fetal Brain Female	brain
11	chr9:8494200-8531200	Weak transcription	Fetal Brain Male	brain
12	chr9:8509400-8528600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:8509800-8532800	Weak transcription	Brain Angular Gyrus	brain
14	chr9:8513200-8523000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:8517000-8522400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:8517000-8523600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:8518000-8528600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:8518200-8526400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:8518400-8526000	Weak transcription	Ovary	ovary
20	chr9:8518400-8533800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr9:8518400-8534000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:8518400-8555200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:8519800-8531600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:8520000-8524000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:8520000-8531200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:8520400-8522400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:8520400-8522600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:8521200-8521600	Genic enhancers	Brain Substantia Nigra	brain
29	chr9:8521200-8521600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
30	chr9:8521200-8521800	Strong transcription	Dnd41	blood
31	chr9:8521200-8522000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:8521200-8522000	Strong transcription	Brain Germinal Matrix	brain
33	chr9:8521200-8522000	Enhancers	Brain Hippocampus Middle	brain
34	chr9:8521200-8522400	Enhancers	Brain Anterior Caudate	brain
35	chr9:8521200-8522400	Strong transcription	Fetal Muscle Leg	muscle
36	chr9:8521200-8525000	Strong transcription	Fetal Lung	lung

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