Variant report

Variant	rs2554888
Chromosome Location	chr15:52831440-52831441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52819614..52823741-chr15:52828078..52832253,5	MCF-7	breast:
2	chr15:52830139..52832000-chr15:52832646..52835396,2	K562	blood:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 222 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:217)

rs_ID	r²[population]
rs1001407	0.80[EUR][1000 genomes]
rs10518691	0.81[AMR][1000 genomes]
rs1075178	0.86[AMR][1000 genomes]
rs10851514	0.81[AMR][1000 genomes]
rs10851515	0.81[AMR][1000 genomes]
rs10851516	0.81[AMR][1000 genomes]
rs10851517	0.81[AMR][1000 genomes]
rs11070898	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11070899	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11070900	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11631183	0.80[EUR][1000 genomes]
rs11852250	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11852261	0.81[AMR][1000 genomes]
rs11852555	0.81[AMR][1000 genomes]
rs11852556	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11852880	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11853078	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11853114	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11853179	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11853337	0.81[AMR][1000 genomes]
rs11853455	0.81[AMR][1000 genomes]
rs11853544	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11853586	0.81[AMR][1000 genomes]
rs11853954	0.89[AMR][1000 genomes]
rs11854130	0.84[AMR][1000 genomes]
rs11854247	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11854405	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11854456	0.81[AMR][1000 genomes]
rs11854480	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11854498	0.81[AMR][1000 genomes]
rs11854642	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11854673	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11854780	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855082	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11855252	0.81[AMR][1000 genomes]
rs11855257	0.81[AMR][1000 genomes]
rs11855295	0.81[AMR][1000 genomes]
rs11855352	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855438	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855453	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11855467	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855584	0.81[AMR][1000 genomes]
rs11855640	0.81[AMR][1000 genomes]
rs11855673	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855692	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11855820	0.81[AMR][1000 genomes]
rs11855884	0.81[AMR][1000 genomes]
rs11856494	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11856542	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11856588	0.83[AMR][1000 genomes]
rs11856626	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11856662	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11856752	0.81[AMR][1000 genomes]
rs11856810	0.81[AMR][1000 genomes]
rs11856912	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11856989	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11857854	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11857914	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11857993	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11858031	0.81[AMR][1000 genomes]
rs11858321	0.81[AMR][1000 genomes]
rs11858927	0.81[AMR][1000 genomes]
rs1464965	0.84[AMR][1000 genomes]
rs1464966	0.84[AMR][1000 genomes]
rs1622405	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1693492	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1693494	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1693497	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1693501	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1693502	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1693505	0.81[EUR][1000 genomes]
rs1693506	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1693507	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1693510	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1693518	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1693522	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1693525	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1693526	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1693527	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1724595	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1724601	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1724603	0.80[EUR][1000 genomes]
rs1724606	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1724608	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1724616	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1724637	0.81[AMR][1000 genomes]
rs17651545	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17651581	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17651611	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17651623	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17651631	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17651692	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17707912	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17707941	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17707984	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17707996	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1815175	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1815176	0.81[AMR][1000 genomes]
rs1869126	0.81[AMR][1000 genomes]
rs1869127	0.81[AMR][1000 genomes]
rs1869128	0.81[AMR][1000 genomes]
rs2049519	0.84[AMR][1000 genomes]
rs2049520	0.84[AMR][1000 genomes]
rs2140962	0.81[AMR][1000 genomes]
rs2177876	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2246134	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257152	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2272283	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2414152	0.81[AMR][1000 genomes]
rs2414155	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2693462	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2693465	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2693466	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28422901	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28519556	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2899488	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2899489	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34003115	0.87[AMR][1000 genomes]
rs34099958	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34113113	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34388417	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36074938	0.81[AMR][1000 genomes]
rs3764227	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4528515	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4547284	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4774624	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4774625	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4774626	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4774627	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4776045	0.81[AMR][1000 genomes]
rs4776048	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4776049	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4776050	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4776051	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4776054	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55663209	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55706220	0.81[AMR][1000 genomes]
rs55710656	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55722736	0.81[AMR][1000 genomes]
rs55774735	0.81[EUR][1000 genomes]
rs55789576	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55842353	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55854724	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55856498	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55876643	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55914546	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55946989	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56017964	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56039749	0.81[AMR][1000 genomes]
rs56043792	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56066720	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56124629	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56128753	0.81[AMR][1000 genomes]
rs56147218	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56148029	0.81[AMR][1000 genomes]
rs56205481	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56206042	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56227135	0.81[AMR][1000 genomes]
rs56271524	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56279946	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56315558	0.81[AMR][1000 genomes]
rs56317843	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56332522	0.84[AMR][1000 genomes]
rs56360952	0.81[AMR][1000 genomes]
rs56749732	0.81[AMR][1000 genomes]
rs56849428	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56850880	0.81[AMR][1000 genomes]
rs57138648	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57364199	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57997370	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58388195	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58922508	0.84[AMR][1000 genomes]
rs59477983	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60248452	0.81[AMR][1000 genomes]
rs60512163	0.81[AMR][1000 genomes]
rs60607997	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61494501	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61617647	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493561	0.80[EUR][1000 genomes]
rs6493563	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66461265	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66674706	0.84[AMR][1000 genomes]
rs66755651	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66870412	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66920283	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67028104	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67249415	0.84[AMR][1000 genomes]
rs67283829	0.81[AMR][1000 genomes]
rs67287941	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67399033	0.81[AMR][1000 genomes]
rs67423475	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67560989	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67632670	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67732354	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67827251	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67876506	0.83[AMR][1000 genomes]
rs68061874	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs68101123	0.81[AMR][1000 genomes]
rs72623982	0.83[AMR][1000 genomes]
rs72623984	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72623985	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72623986	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72623987	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72623988	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72736696	0.81[AMR][1000 genomes]
rs72736701	0.84[AMR][1000 genomes]
rs72736702	0.84[AMR][1000 genomes]
rs72738514	0.80[EUR][1000 genomes]
rs72738516	0.81[EUR][1000 genomes]
rs7402901	0.81[AMR][1000 genomes]
rs8030731	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs940968	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs940971	0.81[AMR][1000 genomes]
rs940972	0.81[AMR][1000 genomes]
rs940973	0.81[AMR][1000 genomes]
rs9788691	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9788777	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2554888	ARPP19	cis	Artery Tibial	GTEx
rs2554888	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs2554888	ARPP19	cis	Nerve Tibial	GTEx
rs2554888	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52822200-52839600	Weak transcription	Right Atrium	heart
2	chr15:52822800-52838400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:52827600-52837200	Weak transcription	A549	lung
4	chr15:52828800-52850400	Weak transcription	Fetal Brain Male	brain
5	chr15:52829800-52832000	Weak transcription	Liver	Liver
6	chr15:52829800-52838000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:52830000-52841200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links