Variant report

Variant	rs7709110
Chromosome Location	chr5:112771323-112771324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YTHDC2-1	chr5:112771263-112772871	ENSG00000232633.3

Extended variants
information (count: 138 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10036300	1.00[JPT][hapmap]
rs10039853	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10040203	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10040430	0.87[ASN][1000 genomes]
rs10046057	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs10061552	0.91[JPT][hapmap]
rs10063334	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10071816	0.84[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs10074538	0.93[EUR][1000 genomes]
rs10079603	0.91[JPT][hapmap]
rs10079758	0.80[ASN][1000 genomes]
rs10079895	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10079973	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10080096	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1017209	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs10477495	0.84[JPT][hapmap]
rs10477497	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10477498	0.80[ASN][1000 genomes]
rs10477499	0.91[JPT][hapmap]
rs10477500	0.91[JPT][hapmap]
rs10478127	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10478129	0.91[JPT][hapmap]
rs10478132	1.00[JPT][hapmap]
rs1052896	0.91[JPT][hapmap]
rs11241210	0.88[ASN][1000 genomes]
rs11241211	0.84[ASN][1000 genomes]
rs11241212	0.84[ASN][1000 genomes]
rs11241214	0.80[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]
rs11241215	0.90[JPT][hapmap]
rs11738075	0.80[CEU][hapmap]
rs11749931	0.80[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs11750488	0.89[AFR][1000 genomes]
rs11956399	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12186798	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12652172	0.80[ASN][1000 genomes]
rs12654189	0.80[ASN][1000 genomes]
rs12660001	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13362066	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1820059	0.84[ASN][1000 genomes]
rs1833680	0.83[ASN][1000 genomes]
rs1833681	0.80[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs1862315	0.84[ASN][1000 genomes]
rs1970798	0.84[ASN][1000 genomes]
rs2162842	0.80[ASN][1000 genomes]
rs2248930	1.00[YRI][hapmap]
rs2288449	0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs26991	0.91[CHB][hapmap];0.83[CHD][hapmap];0.89[YRI][hapmap]
rs28558374	0.80[ASN][1000 genomes]
rs28848005	0.88[ASN][1000 genomes]
rs34514665	0.81[ASN][1000 genomes]
rs34864074	0.81[ASN][1000 genomes]
rs348928	1.00[YRI][hapmap]
rs348929	0.96[YRI][hapmap]
rs348931	0.88[YRI][hapmap]
rs348932	1.00[YRI][hapmap]
rs348938	1.00[YRI][hapmap]
rs348947	1.00[YRI][hapmap]
rs348956	1.00[YRI][hapmap]
rs348961	1.00[YRI][hapmap]
rs348962	1.00[YRI][hapmap]
rs348963	1.00[YRI][hapmap]
rs35162738	0.81[ASN][1000 genomes]
rs367943	1.00[YRI][hapmap]
rs3763138	0.80[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs3763140	0.91[JPT][hapmap]
rs3815911	0.80[CHD][hapmap];0.91[JPT][hapmap]
rs3842917	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3906371	0.84[JPT][hapmap]
rs3906538	0.83[ASN][1000 genomes]
rs3909887	0.84[ASN][1000 genomes]
rs3936061	0.80[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs4334877	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs444322	1.00[YRI][hapmap]
rs455435	1.00[YRI][hapmap]
rs463167	1.00[YRI][hapmap]
rs463249	1.00[YRI][hapmap]
rs4705552	0.81[ASN][1000 genomes]
rs4705553	0.82[ASN][1000 genomes]
rs4705557	1.00[JPT][hapmap]
rs4705820	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705823	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4705825	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs4705827	0.80[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs4705828	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs57530930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58044020	0.80[ASN][1000 genomes]
rs60265545	0.83[ASN][1000 genomes]
rs60810500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60871281	0.80[ASN][1000 genomes]
rs644154	1.00[YRI][hapmap]
rs6594718	0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6594719	0.82[AFR][1000 genomes]
rs6594720	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6594721	0.83[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs6594732	0.80[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs6594733	0.80[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs6594734	0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs67915940	0.82[ASN][1000 genomes]
rs6864278	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6865809	0.89[JPT][hapmap]
rs6876448	0.86[ASN][1000 genomes]
rs6877432	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6878355	0.81[ASN][1000 genomes]
rs6880447	0.83[ASN][1000 genomes]
rs6883383	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs6886628	0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs6887816	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs6889501	0.80[ASN][1000 genomes]
rs6889574	1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs6889783	0.84[ASN][1000 genomes]
rs6898425	0.92[JPT][hapmap]
rs72805422	0.80[ASN][1000 genomes]
rs7349799	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7701913	0.84[ASN][1000 genomes]
rs7705562	1.00[JPT][hapmap]
rs7706215	0.80[ASN][1000 genomes]
rs7706796	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7706958	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7711078	1.00[JPT][hapmap]
rs7711211	0.92[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs7711367	0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs7713038	1.00[JPT][hapmap]
rs7713451	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs7713846	0.83[ASN][1000 genomes]
rs7717644	0.83[ASN][1000 genomes]
rs7729306	0.80[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs7730532	0.80[ASN][1000 genomes]
rs7730557	0.80[ASN][1000 genomes]
rs7730801	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7730949	0.80[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs7732310	0.81[ASN][1000 genomes]
rs7737023	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs919304	0.80[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs929774	1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs9326893	0.91[JPT][hapmap]
rs9654519	0.84[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7709110	YTHDC2	cis	cerebellum	SCAN
rs7709110	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL
rs7709110	YTHDC2	cis	parietal	SCAN
rs7709110	CDO1	cis	cerebellum	SCAN
rs7709110	KCNN2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112762000-112786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:112764400-112779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:112764600-112786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112764800-112786800	Weak transcription	NHEK	skin
5	chr5:112770200-112773800	Enhancers	Fetal Stomach	stomach
6	chr5:112770400-112772200	Enhancers	Fetal Muscle Leg	muscle
7	chr5:112770400-112783400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:112770600-112771800	Enhancers	Right Ventricle	heart
9	chr5:112770600-112772000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:112770600-112773600	Enhancers	Fetal Heart	heart
11	chr5:112770600-112786800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:112770800-112772000	Enhancers	Right Atrium	heart
13	chr5:112770800-112773000	Enhancers	Fetal Brain Male	brain
14	chr5:112770800-112773600	Enhancers	Fetal Lung	lung
15	chr5:112771000-112772000	Enhancers	Fetal Muscle Trunk	muscle
16	chr5:112771200-112771400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:112771200-112771600	Enhancers	Brain Germinal Matrix	brain
18	chr5:112771200-112771600	Enhancers	Ovary	ovary
19	chr5:112771200-112771800	Enhancers	Brain Cingulate Gyrus	brain
20	chr5:112771200-112772000	Enhancers	Left Ventricle	heart

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