Variant report

Variant	rs1476769
Chromosome Location	chr19:42084277-42084278
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42077943..42079577-chr19:42084170..42086427,2	K562	blood:
2	chr19:42078682..42081058-chr19:42082951..42085705,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10420470	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076362	1.00[ASN][1000 genomes]
rs11882144	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745937	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4141218	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4578777	1.00[ASN][1000 genomes]
rs4803480	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs723902	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255679	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs758349	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304595	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1057624	chr19:42057334-42152828	Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1058847	chr19:42057334-42172442	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv519408	chr19:42066279-42171906	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv960930	chr19:42080172-42093112	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv978752	chr19:42082354-42093112	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1476769	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs1476769	CEACAMP3	cis	lung	GTEx
rs1476769	CEACAMP3	cis	Whole Blood	GTEx
rs1476769	CEACAM21	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42082200-42085200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:42082800-42086600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr19:42082800-42086600	Weak transcription	Lung	lung
4	chr19:42083200-42084400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:42083200-42085000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:42083200-42085000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:42083200-42085400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:42083200-42085800	Weak transcription	GM12878-XiMat	blood
9	chr19:42083200-42086600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr19:42083200-42086600	Weak transcription	Thymus	Thymus
11	chr19:42083600-42084400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr19:42083600-42084800	Weak transcription	Primary B cells from cord blood	blood
13	chr19:42083600-42085000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:42083600-42086600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:42083600-42087000	Strong transcription	Primary T cells from cord blood	blood
16	chr19:42083600-42087000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:42083600-42094000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:42083800-42084400	Genic enhancers	Spleen	Spleen
19	chr19:42083800-42084800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:42083800-42086800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:42083800-42088600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr19:42083800-42088600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:42083800-42093600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:42084000-42084800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr19:42084000-42086600	Weak transcription	Placenta	Placenta
26	chr19:42084000-42092000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:42084000-42094200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:42084200-42084400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr19:42084200-42087000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:42084200-42087800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:42084200-42089400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links