Variant report

Variant	rs11852746
Chromosome Location	chr15:55984265-55984266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011061	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs10152116	1.00[ASN][1000 genomes]
rs10152830	1.00[ASN][1000 genomes]
rs10851590	1.00[ASN][1000 genomes]
rs11071203	1.00[ASN][1000 genomes]
rs11632579	0.82[ASN][1000 genomes]
rs11639086	1.00[ASN][1000 genomes]
rs11853533	1.00[ASN][1000 genomes]
rs11857254	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11857271	1.00[ASN][1000 genomes]
rs12438394	1.00[ASN][1000 genomes]
rs12439011	1.00[ASN][1000 genomes]
rs12440103	1.00[ASN][1000 genomes]
rs12442165	1.00[ASN][1000 genomes]
rs12899647	1.00[ASN][1000 genomes]
rs12899976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs12901963	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903239	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905693	1.00[ASN][1000 genomes]
rs12906885	1.00[ASN][1000 genomes]
rs12907557	1.00[ASN][1000 genomes]
rs12907772	1.00[ASN][1000 genomes]
rs12907892	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908232	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12908813	1.00[ASN][1000 genomes]
rs12909497	1.00[CHB][hapmap]
rs12910180	1.00[ASN][1000 genomes]
rs12911682	1.00[ASN][1000 genomes]
rs12912118	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914863	1.00[ASN][1000 genomes]
rs12915092	0.90[ASN][1000 genomes]
rs12915423	1.00[ASN][1000 genomes]
rs1550326	1.00[CHB][hapmap]
rs34303822	1.00[ASN][1000 genomes]
rs3985768	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4412917	1.00[ASN][1000 genomes]
rs4774222	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs491014	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs530798	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs55874929	1.00[ASN][1000 genomes]
rs66519039	1.00[ASN][1000 genomes]
rs689571	1.00[YRI][hapmap]
rs8028880	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8036481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs934886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9920546	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9920680	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11852746	XM_116220	trans	multi-tissue	Pritchard
rs11852746	RFXDC2	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:55932600-55987000	Weak transcription	Ovary	ovary
3	chr15:55954400-55987000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:55960800-55995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:55969000-55987000	Weak transcription	Fetal Lung	lung
6	chr15:55969200-55986000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:55972000-55986400	Weak transcription	Fetal Intestine Large	intestine
8	chr15:55976000-55986400	Weak transcription	Hela-S3	cervix
9	chr15:55976000-55986800	Weak transcription	Fetal Kidney	kidney
10	chr15:55976200-55985800	Weak transcription	A549	lung
11	chr15:55980400-55986200	Weak transcription	GM12878-XiMat	blood
12	chr15:55981000-55987600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:55981200-55985600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:55981200-55985800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:55981200-55986000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:55981200-55986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:55981400-55984400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:55981400-55985600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:55981400-55986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:55982200-55987200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:55982800-55988000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links