Variant report

Variant	rs7252454
Chromosome Location	chr19:42033703-42033704
allele	A/G
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	E2F4	chr19:42033671-42034054	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr19:42033386-42033986	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr19:42033405-42034024	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42031680..42033853-chr19:42037171..42039044,2	K562	blood:
2	chr19:42032930..42034561-chr19:42036519..42039384,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268355	TF binding region
ENSG00000268355	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10406371	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10406545	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10406988	0.82[ASN][1000 genomes]
rs10410081	0.84[ASN][1000 genomes]
rs10423808	0.93[ASN][1000 genomes]
rs10424376	0.93[ASN][1000 genomes]
rs11083626	0.92[ASN][1000 genomes]
rs11668699	0.93[ASN][1000 genomes]
rs11669873	0.84[ASN][1000 genomes]
rs12462897	0.94[ASN][1000 genomes]
rs12609438	0.92[ASN][1000 genomes]
rs2286754	0.92[ASN][1000 genomes]
rs2317312	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3826716	0.94[ASN][1000 genomes]
rs4802120	0.93[ASN][1000 genomes]
rs4802122	0.93[ASN][1000 genomes]
rs4803475	0.85[ASN][1000 genomes]
rs4803476	0.85[ASN][1000 genomes]
rs7248492	0.88[EUR][1000 genomes]
rs7252624	0.92[ASN][1000 genomes]
rs7255742	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257282	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv510767	chr19:41962486-42049165	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv911770	chr19:41962486-42066279	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv911771	chr19:41962486-42085873	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1055515	chr19:41968797-42057334	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv911772	chr19:41985624-42066279	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911773	chr19:42001210-42085873	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv579602	chr19:42015468-42047924	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7252454	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs7252454	CEACAM21	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42029000-42036200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:42029600-42034000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:42029600-42034200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr19:42029600-42034200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:42029600-42034200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr19:42029600-42034800	Weak transcription	Primary B cells from cord blood	blood
7	chr19:42029800-42034600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr19:42029800-42037600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:42033000-42034000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:42033400-42033800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:42033600-42037600	ZNF genes & repeats	GM12878-XiMat	blood

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