Variant report

Variant	rs10938107
Chromosome Location	chr4:74990919-74990920
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr4:74990831-74991054	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr4:74990743-74991067	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr4:74990769-74991072	Hela-S3	cervix:	n/a	n/a
4	TEAD4	chr4:74990841-74991157	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr4:74990849-74991088	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr4:74990730-74991088	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F4	chr4:74990882-74991080	MCF10A-Er-Src	breast:	n/a	n/a
8	ZNF143	chr4:74990821-74991201	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOS	chr4:74990880-74990996	MCF10A-Er-Src	breast:	n/a	chr4:74990891-74990898

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:74962349..74965298-chr4:74989325..74991389,2	K562	blood:

Variant related genes	Relation type
MTHFD2L	TF binding region
ENSG00000081041	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11725704	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11733208	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12642974	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649753	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1371794	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1371795	1.00[ASW][hapmap];0.83[GIH][hapmap]
rs1371798	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs1371799	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs1837559	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1866755	0.87[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs3806792	0.87[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4121652	0.91[EUR][1000 genomes]
rs491641	0.80[CEU][hapmap]
rs518867	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs546829	0.86[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs549280	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72652928	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72652934	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7667376	0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs7686861	0.91[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs882638	0.83[CEU][hapmap]
rs9131	0.83[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs981458	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10938107	UTP3	cis	parietal	SCAN
rs10938107	SNORD59A	trans	cerebellum	SCAN
rs10938107	CCNG2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74987200-74994000	Weak transcription	Thymus	Thymus
2	chr4:74988400-74999600	Weak transcription	NHEK	skin
3	chr4:74989200-74991000	Weak transcription	HMEC	breast
4	chr4:74989400-74999600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:74990200-74996600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:74990400-74995400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:74990600-74991200	Enhancers	Hela-S3	cervix
8	chr4:74990600-74992800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
9	chr4:74990800-74991200	Flanking Active TSS	Liver	Liver

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