Variant report

Variant	rs10406988
Chromosome Location	chr19:42022444-42022445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10406371	0.94[ASN][1000 genomes]
rs10406545	0.94[ASN][1000 genomes]
rs10407939	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap]
rs10410081	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10423808	0.84[EUR][1000 genomes]
rs10424376	0.85[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs11083626	0.84[EUR][1000 genomes]
rs11668699	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11669873	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462897	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12609438	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12973063	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2191139	0.87[JPT][hapmap]
rs2286754	0.84[EUR][1000 genomes]
rs2317312	0.92[ASN][1000 genomes]
rs3826716	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802119	0.81[JPT][hapmap]
rs4802120	0.84[EUR][1000 genomes]
rs4802122	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs4803475	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803476	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248492	0.82[ASN][1000 genomes]
rs7249258	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7252454	0.82[ASN][1000 genomes]
rs7252624	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7255742	0.86[JPT][hapmap]
rs8112363	0.83[JPT][hapmap]
rs8113621	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv3376048	chr19:41969544-42022873	Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3497342	chr19:41969692-42023108	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3497343	chr19:41969692-42023108	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3319145	chr19:41971761-42025822	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3319144	chr19:41971770-42026041	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1060959	chr19:41976648-42023361	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1057764	chr19:41976648-42023588	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv2760512	chr19:41976660-42023600	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	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
14	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
15	nsv579601	chr19:42006714-42031592	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
16	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10406988	R29124_1	cis	multi-tissue	Pritchard
rs10406988	CEACAM21	cis	Whole Blood	GTEx
rs10406988	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs10406988	CEACAM21	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42022200-42023000	Enhancers	Primary B cells from peripheral blood	blood
2	chr19:42022400-42022600	Enhancers	Spleen	Spleen
3	chr19:42022400-42022800	Bivalent Enhancer	HepG2	liver
4	chr19:42022400-42022800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr19:42022400-42023200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:42022400-42023200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:42022400-42023400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
8	chr19:42022400-42023400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr19:42022400-42023600	Enhancers	GM12878-XiMat	blood
10	chr19:42022400-42023800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr19:42022400-42023800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr19:42022400-42024000	Enhancers	Primary B cells from cord blood	blood

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