Variant report

Variant	rs10977054
Chromosome Location	chr9:8405543-8405544
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10815848	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10815850	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10977028	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10977032	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10977037	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10977069	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977075	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977084	0.88[CHB][hapmap]
rs10977089	0.88[CHB][hapmap]
rs12156512	0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344067	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1359117	1.00[JPT][hapmap]
rs7020035	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7040624	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041166	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7044042	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8377800-8406400	Weak transcription	Fetal Brain Female	brain
2	chr9:8389600-8451000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:8394000-8424400	Weak transcription	Fetal Lung	lung
4	chr9:8396000-8410400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:8402000-8408000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:8402200-8407400	Weak transcription	Brain Angular Gyrus	brain
7	chr9:8402400-8407600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:8402400-8407600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:8402400-8407800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:8402400-8407800	Weak transcription	Brain Substantia Nigra	brain
11	chr9:8402400-8408400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:8402400-8408600	Weak transcription	Brain Germinal Matrix	brain
13	chr9:8402400-8421000	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:8402600-8407600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:8402600-8408600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:8402600-8448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:8402800-8438000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:8403200-8407600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:8403400-8408000	Weak transcription	Brain Anterior Caudate	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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