Variant report

Variant	rs12912742
Chromosome Location	chr15:40968531-40968532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10775121	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11070291	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070293	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11631563	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11633269	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11858337	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11858338	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12372947	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12437696	0.82[EUR][1000 genomes]
rs12439683	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12441514	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12442845	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12908284	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2263551	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412546	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2412547	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2412548	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2412549	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2577564	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2619679	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2619680	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2619683	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2917955	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2928140	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3092982	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3101861	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34400306	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs36106105	0.81[EUR][1000 genomes]
rs45495293	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4923884	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4924493	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924495	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4924501	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924503	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56042757	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6492961	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7167854	0.89[ASN][1000 genomes]
rs7169010	0.86[ASN][1000 genomes]
rs7172195	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7173646	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7174551	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7175401	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs752012	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8025883	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8033829	0.80[ASN][1000 genomes]
rs8036817	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12912742	C15orf57	cis	Nerve Tibial	GTEx
rs12912742	C15orf57	cis	Artery Tibial	GTEx
rs12912742	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12912742	CCDC32	cis	multi-tissue	Pritchard
rs12912742	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12912742	C15orf57	cis	lung	GTEx
rs12912742	RP11-111A22.1	cis	lung	GTEx
rs12912742	RAD51	cis	multi-tissue	Pritchard
rs12912742	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs12912742	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12912742	C15orf57	cis	Artery Aorta	GTEx
rs12912742	C15orf57	cis	Esophagus Muscularis	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40913800-40986000	Weak transcription	A549	lung
2	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40955200-40976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:40955200-40983200	Weak transcription	Fetal Intestine Small	intestine
7	chr15:40955800-40976000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:40956800-40971200	Weak transcription	Dnd41	blood
9	chr15:40958600-40981000	Weak transcription	Thymus	Thymus
10	chr15:40960400-40977000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:40968400-40971200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links