Variant report

Variant	rs11833888
Chromosome Location	chr12:59350153-59350154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11172836	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609012	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611254	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11833697	0.86[EUR][1000 genomes]
rs17121746	1.00[CEU][hapmap]
rs17121834	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121856	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121860	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121863	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121866	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121868	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121873	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823337	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59340973	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354920	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354921	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354933	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354937	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73354942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv559048	chr12:59336737-59440659	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11833888	CSDA	trans	brain	seeQTL
rs11833888	SFN	trans	brain	seeQTL
rs11833888	F3	trans	brain	seeQTL
rs11833888	MYBPH	trans	brain	seeQTL
rs11833888	TXNDC5	trans	brain	seeQTL
rs11833888	TAP1	trans	brain	seeQTL
rs11833888	CHI3L1	trans	brain	seeQTL
rs11833888	CXCL11	trans	brain	seeQTL
rs11833888	SCARA3	trans	brain	seeQTL
rs11833888	GADD45A	trans	brain	seeQTL
rs11833888	EMP1	trans	brain	seeQTL
rs11833888	FABP5	trans	brain	seeQTL
rs11833888	NAMPT	trans	brain	seeQTL
rs11833888	MT1A	trans	brain	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59344600-59355000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:59345000-59354000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:59346600-59354000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:59348600-59352600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:59349600-59350200	Enhancers	Duodenum Mucosa	Duodenum
6	chr12:59349600-59351200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:59349600-59351200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:59349800-59350200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:59349800-59350200	Enhancers	Fetal Intestine Large	intestine
10	chr12:59349800-59350400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:59349800-59350400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr12:59349800-59351200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:59349800-59351400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:59350000-59351400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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