Variant report

Variant	rs3826716
Chromosome Location	chr19:42035716-42035717
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	POLR2A	chr19:42035639-42038770	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:42035603-42038761	GM12892	blood:	n/a	n/a
3	SETDB1	chr19:42034208-42038482	U2OS	brain:	n/a	n/a
4	POLR2A	chr19:42035515-42038686	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:42035667-42038718	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000268355	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10406371	0.82[ASN][1000 genomes]
rs10406545	0.83[ASN][1000 genomes]
rs10406988	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10407939	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10410081	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10423808	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10424376	0.90[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083626	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11668699	0.80[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669873	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12150975	0.80[JPT][hapmap]
rs12462897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609438	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12973063	0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap]
rs2191139	0.87[JPT][hapmap]
rs2286754	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317312	0.83[ASN][1000 genomes]
rs2317314	0.81[CHD][hapmap]
rs4802119	0.81[JPT][hapmap]
rs4802120	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802122	0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803475	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803476	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803481	0.80[GIH][hapmap]
rs7249258	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.88[YRI][hapmap]
rs7252454	0.94[ASN][1000 genomes]
rs7252624	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255742	0.81[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7257282	0.88[ASN][1000 genomes]
rs8112363	0.87[JPT][hapmap]
rs8113621	0.94[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3826716	AC011526.1	cis	Adipose Subcutaneous	GTEx
rs3826716	SPHK2	cis	cerebellum	SCAN
rs3826716	CEACAM21	cis	lymphoblastoid	seeQTL
rs3826716	R29124_1	cis	multi-tissue	Pritchard
rs3826716	IRF3	cis	cerebellum	SCAN
rs3826716	FLT3LG	cis	cerebellum	SCAN
rs3826716	CEACAM21	cis	Whole Blood	GTEx
rs3826716	CEACAM21	cis	multi-tissue	Pritchard
rs3826716	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs3826716	SYMPK	cis	cerebellum	SCAN

Chromatin state (count:18 , 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	chr19:42029800-42037600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:42033600-42037600	ZNF genes & repeats	GM12878-XiMat	blood
4	chr19:42034000-42036600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:42034000-42037400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr19:42034200-42036800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr19:42034200-42036800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:42035000-42038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:42035200-42036800	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr19:42035200-42037600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
11	chr19:42035400-42035800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
12	chr19:42035400-42035800	Weak transcription	Spleen	Spleen
13	chr19:42035400-42037200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:42035600-42036200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr19:42035600-42036600	Enhancers	Primary hematopoietic stem cells	blood
16	chr19:42035600-42036600	Bivalent Enhancer	HUVEC	blood vessel
17	chr19:42035600-42037400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:42035600-42037400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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