Variant report

Variant	rs2989509
Chromosome Location	chr9:118001670-118001671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10481680	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs10817733	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs10817734	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs10817741	0.85[CHB][hapmap]
rs10982621	0.81[CHB][hapmap]
rs10982654	0.90[CHB][hapmap]
rs12338583	0.85[CHB][hapmap]
rs1556687	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2183700	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2989508	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2992142	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2992144	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4112338	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs4147051	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs7846857	0.91[CHB][hapmap];0.83[CHD][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	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2989509	AKNA	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117996400-118001800	Weak transcription	Esophagus	oesophagus
2	chr9:117997000-118003800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr9:117999000-118004000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:118000400-118003000	Weak transcription	Fetal Stomach	stomach
5	chr9:118000600-118002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:118000800-118012200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:118001200-118001800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:118001200-118003000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:118001400-118001800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:118001600-118002000	Enhancers	Gastric	stomach
11	chr9:118001600-118002000	Enhancers	NHDF-Ad	bronchial

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Input of quick search could be:

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

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