Variant report

Variant	rs1076362
Chromosome Location	chr19:42091163-42091164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42090966..42093146-chr19:42106951..42108907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239736	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10420470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11882144	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs1476769	1.00[ASN][1000 genomes]
rs1476770	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3745937	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4141218	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4578777	1.00[ASN][1000 genomes]
rs4803480	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs723902	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7255679	0.80[ASN][1000 genomes]
rs758349	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8110782	1.00[JPT][hapmap]
rs9304595	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1076362	CEACAM21	cis	Whole Blood	GTEx
rs1076362	CEACAM21	cis	lymphoblastoid	seeQTL
rs1076362	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs1076362	CEACAMP3	cis	Whole Blood	GTEx
rs1076362	FLT3LG	cis	cerebellum	SCAN
rs1076362	CABP5	cis	cerebellum	SCAN
rs1076362	LMTK3	cis	parietal	SCAN

Chromatin state (count:29 , 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	chr19:42083800-42093600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:42084000-42092000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:42084000-42094200	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr19:42087200-42095000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:42087600-42093800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:42088600-42094600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:42089000-42094200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr19:42089000-42094400	Strong transcription	Primary T cells from cord blood	blood
10	chr19:42089200-42095600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:42089400-42092200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:42089400-42092600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:42089400-42093600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:42089600-42093800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr19:42089600-42093800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:42089600-42094000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:42089600-42095400	Strong transcription	Primary B cells from cord blood	blood
18	chr19:42089600-42101400	Weak transcription	GM12878-XiMat	blood
19	chr19:42089800-42092200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:42089800-42093400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr19:42090200-42093200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:42090200-42093400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr19:42090200-42095400	Strong transcription	Spleen	Spleen
24	chr19:42090400-42094600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:42090600-42092600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr19:42090800-42092800	Weak transcription	Adipose Nuclei	Adipose
27	chr19:42090800-42093000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr19:42091000-42091400	ZNF genes & repeats	Gastric	stomach
29	chr19:42091000-42094200	Weak transcription	Primary hematopoietic stem cells	blood

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