Variant report

Variant	rs2005606
Chromosome Location	chr19:42093112-42093113
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEACAM21-1	chr19:42092817-42093197	NR_110107

Variant related genes	Relation type
ENSG00000239736	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10405039	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10406221	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10420992	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11083627	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11083628	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083629	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673075	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12150975	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12462194	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12983999	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1860255	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2191019	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2302188	0.90[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34054275	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745936	0.82[ASN][1000 genomes]
rs4803479	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803481	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs714106	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7257565	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs873910	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2005606	CEACAMP3	cis	lung	GTEx
rs2005606	R29124_1	cis	multi-tissue	Pritchard
rs2005606	CEACAM21	cis	multi-tissue	Pritchard
rs2005606	CEACAM21	cis	lung	GTEx
rs2005606	CEACAM21	cis	Thyroid	GTEx
rs2005606	CEACAM21	cis	Whole Blood	GTEx
rs2005606	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs2005606	CEACAMP3	cis	Whole Blood	GTEx

Chromatin state (count:30 , 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	chr19:42084000-42094200	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:42087200-42095000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr19:42087600-42093800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:42088600-42094600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:42089000-42094200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr19:42089000-42094400	Strong transcription	Primary T cells from cord blood	blood
9	chr19:42089200-42095600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:42089400-42093600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:42089600-42093800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr19:42089600-42093800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:42089600-42094000	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:42089600-42095400	Strong transcription	Primary B cells from cord blood	blood
15	chr19:42089600-42101400	Weak transcription	GM12878-XiMat	blood
16	chr19:42089800-42093400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr19:42090200-42093200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr19:42090200-42093400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:42090200-42095400	Strong transcription	Spleen	Spleen
20	chr19:42090400-42094600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr19:42091000-42094200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr19:42091400-42093800	Weak transcription	Lung	lung
23	chr19:42091400-42098400	Weak transcription	Gastric	stomach
24	chr19:42092000-42101400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:42092200-42093800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr19:42092200-42096000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:42092600-42095000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr19:42092600-42096800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:42092600-42098400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:42093000-42095600	Weak transcription	Primary monocytes fromperipheralblood	blood

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