Variant report

Variant	rs4578777
Chromosome Location	chr19:42088136-42088137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10420470	1.00[ASN][1000 genomes]
rs1076362	1.00[ASN][1000 genomes]
rs11882144	1.00[ASN][1000 genomes]
rs1476769	1.00[ASN][1000 genomes]
rs1476770	1.00[ASN][1000 genomes]
rs3745937	0.90[ASN][1000 genomes]
rs4141218	1.00[ASN][1000 genomes]
rs4803480	0.87[ASN][1000 genomes]
rs723902	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255679	0.80[ASN][1000 genomes]
rs758349	1.00[ASN][1000 genomes]
rs9304595	1.00[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
rs4578777	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs4578777	CEACAM21	cis	Whole Blood	GTEx
rs4578777	CEACAMP3	cis	lung	GTEx
rs4578777	CEACAMP3	cis	Whole Blood	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42083600-42094000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:42083800-42088600	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr19:42083800-42088600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:42083800-42093600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:42084000-42092000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:42084000-42094200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:42084200-42089400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:42085000-42088200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:42085800-42089600	ZNF genes & repeats	GM12878-XiMat	blood
10	chr19:42086600-42089200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
11	chr19:42086600-42089200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr19:42086600-42089400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:42086600-42089600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:42086600-42089600	ZNF genes & repeats	Placenta	Placenta
15	chr19:42086800-42089200	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr19:42086800-42089400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:42087000-42089000	ZNF genes & repeats	Primary T cells from cord blood	blood
18	chr19:42087000-42089200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:42087000-42089400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr19:42087200-42089800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
21	chr19:42087200-42089800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:42087200-42095000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:42087600-42089200	ZNF genes & repeats	Spleen	Spleen
24	chr19:42087600-42093800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:42087800-42089200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
26	chr19:42088000-42089200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:42088000-42089600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links