Variant report

Variant	rs12902661
Chromosome Location	chr15:72480158-72480159
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1037680	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10518979	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1074330	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11072338	0.82[ASN][1000 genomes]
rs11072339	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072346	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11072351	0.94[ASN][1000 genomes]
rs11852789	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11853101	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11853268	0.81[ASN][1000 genomes]
rs11858015	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12050895	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12439900	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12442886	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12591313	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12591338	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12591426	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592044	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12592364	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12593134	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12593908	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12595228	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12595464	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12898585	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12901580	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901886	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902006	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12903484	0.82[ASN][1000 genomes]
rs12904652	0.81[ASN][1000 genomes]
rs12908882	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12914070	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12916694	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12916951	0.85[ASN][1000 genomes]
rs1384007	0.80[ASN][1000 genomes]
rs16953769	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16956444	0.84[ASN][1000 genomes]
rs16956452	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16956634	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2035379	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2200056	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2279283	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2306488	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2306490	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2415130	0.82[AMR][1000 genomes]
rs2607090	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2856929	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912231	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34137768	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34487006	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35112434	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35115747	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35167572	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35186252	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35206011	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35258998	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35673773	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35713471	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3743224	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3803471	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4131630	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4238449	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4411469	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4445848	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4776584	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4776586	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776589	0.93[ASN][1000 genomes]
rs4777477	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4777478	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4777480	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777484	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4777489	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55854204	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60921026	0.94[ASN][1000 genomes]
rs62025574	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs713048	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71395051	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7169264	0.80[ASN][1000 genomes]
rs7172309	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7182776	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7183196	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7183749	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72733369	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023703	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025504	0.83[ASN][1000 genomes]
rs8028532	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032038	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8192364	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8192386	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8192431	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers 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	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902661	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72477000-72487800	Weak transcription	Esophagus	oesophagus
2	chr15:72477000-72489400	Weak transcription	Right Atrium	heart
3	chr15:72477200-72480800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:72477200-72484400	Weak transcription	NHEK	skin
5	chr15:72477400-72485000	Weak transcription	A549	lung
6	chr15:72479600-72480400	Enhancers	HMEC	breast
7	chr15:72479600-72480600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:72479800-72480200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:72480000-72480400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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