Variant report

Variant	rs11732554
Chromosome Location	chr4:69145677-69145678
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10003465	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005832	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471153	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10866204	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11131746	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11735530	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13118902	0.88[AMR][1000 genomes]
rs13121372	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13127027	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13145544	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13148330	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1406695	0.82[EUR][1000 genomes]
rs1406696	0.82[EUR][1000 genomes]
rs17089240	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17089241	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1715086	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1730872	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1730875	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1880183	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1919905	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1962172	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2140519	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2319790	0.88[AMR][1000 genomes]
rs2319887	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28502119	0.87[ASN][1000 genomes]
rs28692777	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34032921	0.82[EUR][1000 genomes]
rs34186169	0.84[EUR][1000 genomes]
rs34223548	0.82[EUR][1000 genomes]
rs34527218	0.82[EUR][1000 genomes]
rs34896019	0.82[EUR][1000 genomes]
rs35051311	0.84[EUR][1000 genomes]
rs35572241	0.88[AMR][1000 genomes]
rs4860292	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4860927	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4860932	0.80[EUR][1000 genomes]
rs4860933	0.82[EUR][1000 genomes]
rs4860934	0.82[EUR][1000 genomes]
rs56264769	0.88[AMR][1000 genomes]
rs62316198	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62316204	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6822778	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7658151	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7671950	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672364	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678448	1.00[ASN][1000 genomes]
rs7696268	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991215	0.92[AMR][1000 genomes];0.92[EUR][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	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1812438	chr4:68943858-69154222	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv964740	chr4:69137797-69159003	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11732554	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69139400-69149600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:69139600-69147400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:69139600-69153600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:69140400-69145800	Weak transcription	Fetal Intestine Small	intestine
5	chr4:69140400-69146000	Weak transcription	Fetal Intestine Large	intestine
6	chr4:69144000-69148400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:69144000-69149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:69144400-69148600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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