Variant report

Variant	rs12108098
Chromosome Location	chr3:61512919-61512920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12491377	0.90[EUR][1000 genomes]
rs2886521	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61269136	0.83[EUR][1000 genomes]
rs73093079	0.90[EUR][1000 genomes]
rs73094710	0.90[EUR][1000 genomes]
rs73111553	0.92[EUR][1000 genomes]
rs73111557	0.92[EUR][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	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12108098	ADAMTS9	cis	parietal	SCAN
rs12108098	FHIT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61508600-61516200	Weak transcription	Fetal Kidney	kidney
2	chr3:61508600-61517000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:61511000-61515800	Weak transcription	Fetal Heart	heart
4	chr3:61511400-61513000	Weak transcription	Right Ventricle	heart
5	chr3:61512200-61513000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:61512400-61513400	Weak transcription	Placenta	Placenta
7	chr3:61512400-61516200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:61512400-61516200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:61512400-61516400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:61512800-61513200	Enhancers	Left Ventricle	heart
11	chr3:61512800-61516000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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