Variant report

Variant	rs12904801
Chromosome Location	chr15:40964435-40964436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1037445	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10400890	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10400901	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10444817	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070282	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070285	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070286	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632061	0.81[EUR][1000 genomes]
rs11632370	0.81[EUR][1000 genomes]
rs11852670	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11852694	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11852828	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11854986	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855334	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855923	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11856802	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858113	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858938	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591207	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902568	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905162	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12912635	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913697	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12914743	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16970851	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1813898	0.81[EUR][1000 genomes]
rs1967368	0.84[EUR][1000 genomes]
rs2412531	0.81[EUR][1000 genomes]
rs2412532	0.81[EUR][1000 genomes]
rs2412544	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898996	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2924387	0.86[EUR][1000 genomes]
rs3092979	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34845954	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35047458	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751652	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3751653	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4080706	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4410047	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923876	0.81[EUR][1000 genomes]
rs4924481	0.81[EUR][1000 genomes]
rs62019916	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62019918	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582	0.81[EUR][1000 genomes]
rs71471881	0.85[EUR][1000 genomes]
rs7169621	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181074	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182530	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183790	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026605	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8029384	0.81[EUR][1000 genomes]
rs8034043	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8034048	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8036737	0.84[EUR][1000 genomes]
rs8038407	0.85[EUR][1000 genomes]
rs8041534	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs896795	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs12904801	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12904801	C15orf57	cis	Nerve Tibial	GTEx
rs12904801	C15orf57	cis	Thyroid	GTEx
rs12904801	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12904801	C15orf57	cis	Artery Tibial	GTEx
rs12904801	C15orf57	cis	Artery Aorta	GTEx
rs12904801	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12904801	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12904801	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs12904801	C15orf57	cis	Muscle Skeletal	GTEx
rs12904801	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12904801	C15orf57	cis	Esophagus Mucosa	GTEx
rs12904801	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12904801	C15orf57	cis	Stomach	GTEx
rs12904801	RP11-111A22.1	cis	lung	GTEx
rs12904801	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12904801	C15orf57	cis	Esophagus Muscularis	GTEx
rs12904801	C15orf57	cis	Heart Left Ventricle	GTEx
rs12904801	C15orf57	cis	lung	GTEx
rs12904801	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs12904801	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs12904801	RP11-111A22.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:14 , 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	chr15:40956800-40966000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr15:40956800-40971200	Weak transcription	Dnd41	blood
10	chr15:40958400-40966600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:40958600-40981000	Weak transcription	Thymus	Thymus
12	chr15:40960400-40977000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:40964400-40965200	Enhancers	Primary B cells from peripheral blood	blood
14	chr15:40964400-40965400	Enhancers	GM12878-XiMat	blood

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