Variant report

Variant	rs56030143
Chromosome Location	chr5:112941866-112941867
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 164 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10036298	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10036300	0.81[EUR][1000 genomes]
rs10038632	0.86[ASN][1000 genomes]
rs10039853	0.80[ASN][1000 genomes]
rs10040203	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10040430	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10040516	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10042563	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10043066	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10046057	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10052077	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10053582	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10061552	0.84[ASN][1000 genomes]
rs10063008	0.87[ASN][1000 genomes]
rs10065616	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10071816	0.80[ASN][1000 genomes]
rs10072547	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10076131	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10079603	0.84[ASN][1000 genomes]
rs10079758	0.80[ASN][1000 genomes]
rs10079895	0.80[ASN][1000 genomes]
rs10079973	0.80[ASN][1000 genomes]
rs10080096	0.80[ASN][1000 genomes]
rs1017209	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1035888	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10477495	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10477497	0.80[ASN][1000 genomes]
rs10477498	0.80[ASN][1000 genomes]
rs10477499	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10477500	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10478126	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10478127	0.80[ASN][1000 genomes]
rs10478129	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10478132	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1052896	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1080858	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241210	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11241211	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11241212	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11241214	0.84[ASN][1000 genomes]
rs11241215	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11742968	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749931	0.80[ASN][1000 genomes]
rs11956399	0.80[ASN][1000 genomes]
rs12186798	0.80[ASN][1000 genomes]
rs12514105	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12516911	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12519315	0.88[AMR][1000 genomes]
rs12652172	0.80[ASN][1000 genomes]
rs12654189	0.80[ASN][1000 genomes]
rs12660001	0.80[ASN][1000 genomes]
rs13359625	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13359648	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13359652	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13359703	0.86[ASN][1000 genomes]
rs13362066	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1549628	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17135766	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135776	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1820059	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1833680	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1833681	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1862315	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1970798	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2115216	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2162842	0.80[ASN][1000 genomes]
rs2162847	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288449	0.86[ASN][1000 genomes]
rs2416319	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28558374	0.80[ASN][1000 genomes]
rs28848005	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2900072	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3763138	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763140	0.87[ASN][1000 genomes]
rs3815911	0.85[ASN][1000 genomes]
rs3842917	0.84[EUR][1000 genomes]
rs3906538	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3909887	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4122547	0.87[EUR][1000 genomes]
rs4132093	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4588592	0.87[ASN][1000 genomes]
rs4705552	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4705555	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705556	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705557	0.86[ASN][1000 genomes]
rs4705823	0.85[EUR][1000 genomes]
rs4705825	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4705827	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4705828	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4705832	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705833	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56206672	0.86[ASN][1000 genomes]
rs57134656	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58044020	0.80[ASN][1000 genomes]
rs58391392	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59958489	0.88[AFR][1000 genomes]
rs60265545	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60871281	0.80[ASN][1000 genomes]
rs60914066	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6594718	0.83[EUR][1000 genomes]
rs6594719	0.84[EUR][1000 genomes]
rs6594720	0.82[EUR][1000 genomes]
rs6594721	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6594729	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6594732	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6594733	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6594734	0.80[ASN][1000 genomes]
rs6594738	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67915940	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6865809	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6867502	0.86[ASN][1000 genomes]
rs6876448	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6877432	0.80[ASN][1000 genomes]
rs6877466	0.86[ASN][1000 genomes]
rs6877834	0.86[ASN][1000 genomes]
rs6878282	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878355	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6878900	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880447	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6883383	0.87[ASN][1000 genomes]
rs6883557	0.87[ASN][1000 genomes]
rs6886628	0.84[ASN][1000 genomes]
rs6887816	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6889501	0.80[ASN][1000 genomes]
rs6889574	0.80[ASN][1000 genomes]
rs6889783	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6898425	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72805422	0.80[ASN][1000 genomes]
rs754573	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7701913	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7704170	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706215	0.80[ASN][1000 genomes]
rs7706796	0.82[EUR][1000 genomes]
rs7706958	0.80[ASN][1000 genomes]
rs7707895	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7711078	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7711211	0.80[ASN][1000 genomes]
rs7711367	0.80[ASN][1000 genomes]
rs7713038	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713451	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7713846	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7715601	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7717644	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7722918	0.86[ASN][1000 genomes]
rs7723108	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7729306	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7730532	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7730557	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7730949	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7732310	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7737023	0.80[ASN][1000 genomes]
rs919304	0.87[ASN][1000 genomes]
rs929774	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9326893	0.84[ASN][1000 genomes]
rs9326897	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9654519	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9885245	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv520674	chr5:112911165-112942820	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
rs56030143	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL
rs56030143	YTHDC2	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112910600-112942000	Weak transcription	Brain Substantia Nigra	brain
2	chr5:112910800-112942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:112917200-112942000	Weak transcription	K562	blood
4	chr5:112920800-112942000	Weak transcription	Ovary	ovary
5	chr5:112929800-112942000	Weak transcription	NH-A	brain
6	chr5:112929800-112943800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:112930000-112942000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:112930000-112942200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:112930000-112943800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:112930000-112944000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:112930200-112942000	Weak transcription	Left Ventricle	heart
12	chr5:112930200-112944000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:112930400-112942000	Weak transcription	A549	lung
14	chr5:112930800-112942200	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:112931400-112943600	Weak transcription	NHDF-Ad	bronchial
16	chr5:112931800-112943600	Weak transcription	Dnd41	blood
17	chr5:112932600-112942200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:112933600-112942000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:112933800-112943800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:112939400-112942000	Weak transcription	HMEC	breast
21	chr5:112939600-112942200	Weak transcription	NHEK	skin
22	chr5:112941400-112942000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:112941400-112942200	Weak transcription	Fetal Heart	heart
24	chr5:112941400-112942400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr5:112941800-112942000	Enhancers	Brain Cingulate Gyrus	brain
26	chr5:112941800-112942000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:112941800-112942000	Enhancers	Right Atrium	heart
28	chr5:112941800-112942400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr5:112941800-112942400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:112941800-112942400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:112941800-112942400	Enhancers	Placenta	Placenta
32	chr5:112941800-112942400	Flanking Active TSS	HUVEC	blood vessel

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