Variant report

Variant	rs3903826
Chromosome Location	chr9:8408803-8408804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10815872	1.00[YRI][hapmap]
rs10977047	0.82[AMR][1000 genomes]
rs10977050	0.81[AMR][1000 genomes]
rs1875239	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs3847293	1.00[YRI][hapmap];0.81[AMR][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	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
4	nsv973439	chr9:8406003-8408876	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	nsv613287	chr9:8408453-8422302	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3903826	CDC37L1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8389600-8451000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:8394000-8424400	Weak transcription	Fetal Lung	lung
3	chr9:8396000-8410400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:8402400-8421000	Weak transcription	Brain Hippocampus Middle	brain
5	chr9:8402600-8448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:8402800-8438000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:8405800-8438000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:8407600-8410800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr9:8407600-8410800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr9:8407800-8410600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:8407800-8414600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:8408000-8410600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:8408200-8409400	Weak transcription	Brain Angular Gyrus	brain
14	chr9:8408200-8409800	Weak transcription	Brain Substantia Nigra	brain
15	chr9:8408200-8429200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:8408400-8409200	Enhancers	Dnd41	blood
17	chr9:8408400-8410400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr9:8408400-8410600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:8408600-8409400	Enhancers	H9 Cell Line	embryonic stem cell
20	chr9:8408600-8409400	Enhancers	Fetal Thymus	thymus
21	chr9:8408600-8410600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:8408600-8410600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr9:8408600-8410600	Enhancers	Brain Germinal Matrix	brain
24	chr9:8408800-8409200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:8408800-8409800	Weak transcription	Brain Anterior Caudate	brain
26	chr9:8408800-8410600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:8408800-8410800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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