Variant report

Variant	rs12584122
Chromosome Location	chr13:50478967-50478968
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-3	chr13:50478837-50479046	NONHSAT033764

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1063181	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1063183	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100038	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12100048	1.00[JPT][hapmap]
rs12583615	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12583637	0.81[EUR][1000 genomes]
rs12583652	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12583823	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12584069	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12585966	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17073655	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17073682	0.82[EUR][1000 genomes]
rs17073724	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1807033	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2066540	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2066546	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2066547	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2066552	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2066553	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2066555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2177313	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs2181267	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181268	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2407881	0.81[EUR][1000 genomes]
rs2407882	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs41308548	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4614628	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55638467	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55727821	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55869555	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57230741	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59086590	0.84[EUR][1000 genomes]
rs59931782	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60574696	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60583460	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60828549	0.81[AFR][1000 genomes]
rs61960398	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960442	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960445	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960446	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960447	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61960449	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960450	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960451	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960454	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs61960455	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs61960457	0.83[EUR][1000 genomes]
rs61961261	0.83[EUR][1000 genomes]
rs61961263	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61961294	0.91[EUR][1000 genomes]
rs61961298	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61961299	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61961302	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61961324	0.81[AFR][1000 genomes]
rs6561571	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6561572	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6561575	1.00[JPT][hapmap]
rs66756338	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7319351	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73194486	0.95[ASN][1000 genomes]
rs73196708	0.90[ASN][1000 genomes]
rs73196731	0.81[EUR][1000 genomes]
rs732729	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7328892	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7334063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7336477	0.89[EUR][1000 genomes]
rs7339181	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs74078717	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7982125	1.00[JPT][hapmap]
rs7984332	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7986364	0.85[CEU][hapmap];0.81[AFR][1000 genomes]
rs7986432	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7990502	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7991454	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7992903	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7994224	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7995557	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7997305	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7997402	0.83[EUR][1000 genomes]
rs7997638	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7998223	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs7998391	0.81[EUR][1000 genomes]
rs9670083	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1851738	chr13:50474326-50507944	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12584122	TRIM13	cis	Nerve Tibial	GTEx
rs12584122	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs12584122	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50468600-50486000	Weak transcription	Liver	Liver
2	chr13:50476400-50497400	Weak transcription	Pancreas	Pancrea
3	chr13:50477000-50479000	Weak transcription	HepG2	liver
4	chr13:50477800-50499600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr13:50478000-50487200	Weak transcription	Ovary	ovary
6	chr13:50478000-50495200	Weak transcription	Brain Hippocampus Middle	brain
7	chr13:50478600-50491400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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