Variant report

Variant	rs12292915
Chromosome Location	chr11:18038118-18038119
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZC3H11A	chr11:18038060-18038220	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:18037112..18038638-chr11:18097036..18099168,2	K562	blood:
2	chr11:18033853..18039770-chr11:18040771..18045725,5	K562	blood:
3	chr11:18025939..18028718-chr11:18036280..18038941,2	K562	blood:

Variant related genes	Relation type
SERGEF	TF binding region
ENSG00000129158	Chromatin interaction
ENSG00000129167	Chromatin interaction
ENSG00000255448	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10488683	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10766450	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12277387	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap]
rs172424	0.96[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs1914710	0.96[CEU][hapmap]
rs2108977	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211114	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs211115	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs211128	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs211130	0.96[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs211131	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs211135	0.96[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs211136	0.88[EUR][1000 genomes]
rs211137	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2137777	0.96[CEU][hapmap]
rs2237923	0.91[CEU][hapmap]
rs2283238	0.96[CEU][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap]
rs2283240	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs2299623	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs371589	0.96[CEU][hapmap]
rs3741200	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3741201	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741202	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3958112	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4757603	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs4757607	0.95[CEU][hapmap]
rs484616	0.96[CEU][hapmap];0.81[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12292915	SERGEF	cis	Adipose Subcutaneous	GTEx
rs12292915	RP1-59M18.2	cis	Muscle Skeletal	GTEx
rs12292915	SERGEF	cis	Muscle Skeletal	GTEx
rs12292915	SERGEF	cis	lung	GTEx
rs12292915	SAAL1	cis	cerebellum	SCAN
rs12292915	KCNC1	cis	parietal	SCAN
rs12292915	SAAL1	cis	parietal	SCAN
rs12292915	RP1-59M18.2	cis	Adipose Subcutaneous	GTEx
rs12292915	SERGEF	cis	Esophagus Mucosa	GTEx
rs12292915	SAAL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18035600-18038400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:18035600-18048600	Weak transcription	Ovary	ovary
3	chr11:18036000-18040000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:18036000-18046000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:18036400-18041000	Weak transcription	Aorta	Aorta
6	chr11:18036800-18045400	Weak transcription	HepG2	liver
7	chr11:18038000-18039000	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links