Variant report

Variant	rs10003465
Chromosome Location	chr4:69148723-69148724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10005832	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471153	0.81[EUR][1000 genomes]
rs10866204	0.83[EUR][1000 genomes]
rs11131746	0.81[EUR][1000 genomes]
rs11732554	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735530	0.81[EUR][1000 genomes]
rs12331971	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13112407	0.82[AMR][1000 genomes]
rs13121372	0.81[EUR][1000 genomes]
rs13127027	0.81[EUR][1000 genomes]
rs13145544	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13148330	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320797	0.85[EUR][1000 genomes]
rs17089240	0.81[EUR][1000 genomes]
rs17089241	0.81[EUR][1000 genomes]
rs1962172	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28502119	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28692777	0.87[ASN][1000 genomes]
rs34282559	0.85[EUR][1000 genomes]
rs34749553	0.81[AMR][1000 genomes]
rs3927373	0.91[EUR][1000 genomes]
rs4860928	0.86[EUR][1000 genomes]
rs62316198	0.87[ASN][1000 genomes]
rs62316204	0.81[EUR][1000 genomes]
rs6552177	0.81[AMR][1000 genomes]
rs6552178	0.81[AMR][1000 genomes]
rs6552179	0.86[EUR][1000 genomes]
rs7670560	0.82[AMR][1000 genomes]
rs7671950	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672364	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680622	0.81[AMR][1000 genomes]
rs7689802	0.81[AMR][1000 genomes]
rs7696268	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953794	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs953795	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9990842	0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[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
rs10003465	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr4:69139600-69153600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:69144000-69149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:69147200-69149000	Enhancers	K562	blood
5	chr4:69147200-69149400	Enhancers	Fetal Intestine Small	intestine
6	chr4:69148000-69149400	Enhancers	Fetal Intestine Large	intestine
7	chr4:69148200-69148800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:69148200-69148800	Enhancers	HepG2	liver
9	chr4:69148400-69149400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:69148600-69149200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:69148600-69151600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links