Variant report

Variant	rs2417678
Chromosome Location	chr9:108728366-108728367
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10733558	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759156	0.97[ASN][1000 genomes]
rs10816354	0.81[ASN][1000 genomes]
rs10816356	0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10978361	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10978362	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984676	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2417677	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2900407	0.89[ASN][1000 genomes]
rs4076012	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4609252	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4742659	0.82[ASN][1000 genomes]
rs55721325	0.90[ASN][1000 genomes]
rs55735471	0.90[ASN][1000 genomes]
rs7866652	0.91[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	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1041073	chr9:108535813-108731343	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1052684	chr9:108582944-108730280	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831679	chr9:108603112-108785347	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1047166	chr9:108693810-108921872	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108720600-108731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:108722000-108729000	Weak transcription	Brain Substantia Nigra	brain
3	chr9:108726000-108731200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:108726200-108731200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:108726400-108729000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:108726400-108730200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:108726600-108730000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:108726600-108730200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:108726800-108730200	Weak transcription	Brain Angular Gyrus	brain
10	chr9:108726800-108730800	Weak transcription	Brain Anterior Caudate	brain
11	chr9:108726800-108736800	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:108727000-108728800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:108727000-108729600	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:108727000-108731400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:108728200-108729400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:108728200-108732600	Enhancers	Fetal Brain Male	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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