Variant report

Variant	rs2286754
Chromosome Location	chr19:42042331-42042332
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42035785..42038762-chr19:42042099..42044984,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEACAM21-2	chr19:42041545-42043262	ENSG00000270164.1

Variant related genes	Relation type
ENSG00000268355	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10406988	0.84[EUR][1000 genomes]
rs10410081	0.84[EUR][1000 genomes]
rs10423808	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10424376	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083626	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668699	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11669873	0.84[EUR][1000 genomes]
rs12462897	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12609438	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2317312	0.81[ASN][1000 genomes]
rs3826716	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802120	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802122	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803475	0.84[EUR][1000 genomes]
rs4803476	0.84[EUR][1000 genomes]
rs7252454	0.92[ASN][1000 genomes]
rs7252624	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7255742	0.94[ASN][1000 genomes]
rs7257282	0.97[ASN][1000 genomes]
rs8113621	0.92[ASN][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	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
8	nsv978751	chr19:42036596-42073874	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2286754	CEACAM21	cis	Whole Blood	GTEx
rs2286754	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs2286754	AC011526.1	cis	Thyroid	GTEx
rs2286754	AC011526.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42038600-42042800	Weak transcription	Right Atrium	heart
2	chr19:42038600-42044400	Weak transcription	Thymus	Thymus
3	chr19:42038600-42050800	Weak transcription	Spleen	Spleen
4	chr19:42040200-42044000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:42040400-42042800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr19:42041600-42043000	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr19:42041800-42043200	Flanking Active TSS	GM12878-XiMat	blood
8	chr19:42042000-42042800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr19:42042000-42043800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr19:42042000-42044000	Weak transcription	Adipose Nuclei	Adipose
11	chr19:42042000-42046600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:42042200-42042400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr19:42042200-42044000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:42042200-42048400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:42042200-42048600	Weak transcription	Primary T cells from cord blood	blood
16	chr19:42042200-42048600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:42042200-42048600	Weak transcription	Monocytes-CD14+_RO01746	blood

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