Variant report

Variant	rs12708404
Chromosome Location	chr15:45767079-45767080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12907319	1.00[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12910629	1.00[ASN][1000 genomes]
rs12915009	1.00[ASN][1000 genomes]
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	1.00[YRI][hapmap]
rs8029246	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	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
3	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1523	chr15:45749900-45783825	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12708404	GATM	cis	cerebellum	SCAN
rs12708404	BMF	cis	parietal	SCAN
rs12708404	SLC30A4	cis	parietal	SCAN
rs12708404	C15orf52	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45750800-45781000	Weak transcription	Stomach Mucosa	stomach
2	chr15:45751200-45801600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:45754200-45801600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:45757000-45794600	Weak transcription	Colonic Mucosa	Colon
5	chr15:45757000-45801800	Weak transcription	Gastric	stomach
6	chr15:45759800-45768600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:45760800-45772800	Weak transcription	HSMMtube	muscle
8	chr15:45761000-45768800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:45761800-45768400	Weak transcription	Fetal Intestine Small	intestine
10	chr15:45762000-45773800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:45762400-45768200	Weak transcription	Fetal Intestine Large	intestine
12	chr15:45763400-45777200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr15:45767000-45767200	Flanking Bivalent TSS/Enh	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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