Variant report

Variant	rs12907319
Chromosome Location	chr15:45815975-45815976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12708404	1.00[ASN][1000 genomes]
rs12899310	0.81[AMR][1000 genomes]
rs12910629	1.00[ASN][1000 genomes]
rs12915009	1.00[ASN][1000 genomes]
rs2453531	0.81[GIH][hapmap]
rs2733249	1.00[ASN][1000 genomes]
rs35394591	1.00[ASN][1000 genomes]
rs35707605	1.00[ASN][1000 genomes]
rs6493163	1.00[ASN][1000 genomes]
rs7496542	1.00[ASN][1000 genomes]
rs8025019	0.82[MEX][hapmap];1.00[YRI][hapmap]
rs8029246	1.00[ASW][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][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	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1045556	chr15:45777396-45884854	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12907319	GATM	cis	cerebellum	SCAN
rs12907319	BMF	cis	parietal	SCAN
rs12907319	C15orf52	cis	parietal	SCAN
rs12907319	SHF	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45814200-45816000	Active TSS	Rectal Smooth Muscle	rectum
2	chr15:45814400-45816000	Active TSS	NH-A	brain
3	chr15:45815400-45816000	Active TSS	Brain Germinal Matrix	brain
4	chr15:45815600-45816000	Enhancers	Fetal Stomach	stomach
5	chr15:45815600-45816000	Enhancers	Stomach Mucosa	stomach
6	chr15:45815600-45818400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr15:45815600-45825000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:45815800-45816000	Enhancers	Fetal Brain Male	brain
9	chr15:45815800-45816000	Enhancers	Fetal Brain Female	brain
10	chr15:45815800-45816000	Enhancers	Fetal Muscle Trunk	muscle
11	chr15:45815800-45818400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:45815800-45819000	Weak transcription	Duodenum Mucosa	Duodenum

Quick Search:

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

what's new

Quick links