Variant report

Variant	rs10042563
Chromosome Location	chr5:112943948-112943949
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10036298	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10038632	0.81[ASN][1000 genomes]
rs10040203	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10040430	0.86[EUR][1000 genomes]
rs10040516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10043066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10046057	0.86[EUR][1000 genomes]
rs10052077	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10053582	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10063008	0.82[ASN][1000 genomes]
rs10065616	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10072547	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10076131	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1017209	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1035888	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10477495	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10477499	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10477500	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10478126	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10478129	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10478132	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1052896	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1080858	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11241210	0.86[EUR][1000 genomes]
rs11241211	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11241212	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11241215	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11742968	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12514105	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12516911	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12519315	0.85[AMR][1000 genomes]
rs13359625	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13359648	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13359652	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13359703	0.81[ASN][1000 genomes]
rs13362066	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1549628	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17135766	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17135776	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1820059	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1833680	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1833681	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1862315	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1970798	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2115216	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2162847	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288449	0.81[ASN][1000 genomes]
rs2416319	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28848005	0.86[EUR][1000 genomes]
rs2900072	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3763138	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3763140	0.82[ASN][1000 genomes]
rs3815911	0.80[ASN][1000 genomes]
rs3906538	0.84[EUR][1000 genomes]
rs3909887	0.84[EUR][1000 genomes]
rs4122547	0.83[EUR][1000 genomes]
rs4132093	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4588592	0.82[ASN][1000 genomes]
rs4705552	0.87[EUR][1000 genomes]
rs4705555	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705556	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705557	0.81[ASN][1000 genomes]
rs4705823	0.81[EUR][1000 genomes]
rs4705825	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4705827	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705828	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705832	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4705833	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56030143	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56206672	0.81[ASN][1000 genomes]
rs57134656	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58391392	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59958489	0.84[AFR][1000 genomes]
rs60265545	0.84[EUR][1000 genomes]
rs6594721	0.86[EUR][1000 genomes]
rs6594729	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6594732	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6594733	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6594738	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67915940	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6865809	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6867502	0.81[ASN][1000 genomes]
rs6876448	0.86[EUR][1000 genomes]
rs6877466	0.81[ASN][1000 genomes]
rs6877834	0.81[ASN][1000 genomes]
rs6878282	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6878355	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6878900	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6880447	0.86[EUR][1000 genomes]
rs6883383	0.82[ASN][1000 genomes]
rs6883557	0.82[ASN][1000 genomes]
rs6887816	0.86[EUR][1000 genomes]
rs6889783	0.84[EUR][1000 genomes]
rs6898425	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs754573	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7701913	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7704170	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7707895	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7711078	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7713038	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7713451	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7713846	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7715601	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7717644	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7722918	0.81[ASN][1000 genomes]
rs7723108	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7729306	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7730532	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7730557	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7730949	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7732310	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs919304	0.82[ASN][1000 genomes]
rs929774	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9326897	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9654519	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9885245	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv882721	chr5:112859994-112963488	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv1033202	chr5:112891857-112945992	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	esv2752057	chr5:112916398-112945992	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1029507	chr5:112916398-112945992	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	esv2763910	chr5:112916398-112951827	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1031336	chr5:112916398-112956588	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10042563	YTHDC2	cis	multi-tissue	Pritchard
rs10042563	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112930000-112944000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:112930200-112944000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:112943200-112944200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr5:112943600-112944200	Enhancers	Dnd41	blood
5	chr5:112943600-112944200	Enhancers	HSMMtube	muscle
6	chr5:112943600-112944200	Enhancers	NHDF-Ad	bronchial
7	chr5:112943600-112944400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:112943800-112944000	Enhancers	Hela-S3	cervix
9	chr5:112943800-112944200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:112943800-112944200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:112943800-112944200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr5:112943800-112944200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:112943800-112944200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:112943800-112944200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:112943800-112944200	Enhancers	HUVEC	blood vessel
16	chr5:112943800-112944400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:112943800-112944400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:112943800-112944400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:112943800-112944400	Enhancers	Left Ventricle	heart
20	chr5:112943800-112944400	Enhancers	HMEC	breast
21	chr5:112943800-112944400	Enhancers	K562	blood
22	chr5:112943800-112944400	Enhancers	Osteobl	bone

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