Variant report

Variant	rs7678448
Chromosome Location	chr4:69151046-69151047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10003465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005832	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471153	0.83[EUR][1000 genomes]
rs10866204	0.81[EUR][1000 genomes]
rs11131746	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11732554	1.00[ASN][1000 genomes]
rs11735530	1.00[CEU][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs12331971	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13112407	0.82[AMR][1000 genomes]
rs13121372	0.82[EUR][1000 genomes]
rs13127027	0.82[EUR][1000 genomes]
rs13145544	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13148330	1.00[ASN][1000 genomes]
rs1320797	0.86[EUR][1000 genomes]
rs17089240	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17089241	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1962172	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28502119	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28692777	0.87[ASN][1000 genomes]
rs34282559	0.86[EUR][1000 genomes]
rs34749553	0.81[AMR][1000 genomes]
rs3927373	0.93[EUR][1000 genomes]
rs4860928	0.88[EUR][1000 genomes]
rs4860930	0.81[EUR][1000 genomes]
rs62316198	0.87[ASN][1000 genomes]
rs62316204	0.83[EUR][1000 genomes]
rs6552177	0.81[AMR][1000 genomes]
rs6552178	0.81[AMR][1000 genomes]
rs6552179	0.88[EUR][1000 genomes]
rs7670560	1.00[CHD][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs7671950	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672364	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680622	0.81[AMR][1000 genomes]
rs7689802	0.81[AMR][1000 genomes]
rs7696268	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953794	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs953795	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9990842	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9991215	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7678448	UTP3	cis	cerebellum	SCAN
rs7678448	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69139600-69153600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:69148600-69151600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:69149000-69151200	Enhancers	NHEK	skin
4	chr4:69149400-69153600	Weak transcription	Fetal Intestine Large	intestine
5	chr4:69149400-69153600	Weak transcription	Fetal Intestine Small	intestine
6	chr4:69150600-69151200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr4:69150600-69151400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:69150600-69151800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:69150800-69151200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr4:69150800-69151200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:69150800-69151200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr4:69151000-69153400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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