Variant report

Variant	rs11174770
Chromosome Location	chr12:63480196-63480197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11174764	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11174771	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1495029	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2358603	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes]
rs4587779	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes]
rs4763058	0.90[CHB][hapmap]
rs7138381	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7312819	0.89[AMR][1000 genomes];0.83[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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2751108	chr12:63445933-63503952	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11174770	ARHGEF25	cis	parietal	SCAN
rs11174770	USP15	cis	cerebellum	SCAN
rs11174770	TSPAN31	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63472800-63480400	Enhancers	Fetal Intestine Small	intestine
2	chr12:63473400-63480600	Enhancers	Fetal Intestine Large	intestine
3	chr12:63474200-63485800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:63475200-63487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:63477000-63480400	Enhancers	Fetal Kidney	kidney
6	chr12:63477600-63480600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr12:63477600-63480600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr12:63477600-63480600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:63477600-63481400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:63477800-63480200	Weak transcription	Gastric	stomach
11	chr12:63478200-63480400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr12:63478600-63480400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:63479000-63480200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:63479200-63480400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:63479400-63480200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:63479800-63480400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:63479800-63480600	Enhancers	Stomach Mucosa	stomach
18	chr12:63480000-63481200	Enhancers	Liver	Liver
19	chr12:63480000-63485400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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