Variant report

Variant	rs11083628
Chromosome Location	chr19:42077832-42077833
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	CTCF	chr19:42077700-42077850	NHDF-neo	bronchial:	n/a	n/a
2	CTCF	chr19:42077760-42077910	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr19:42077760-42077910	BJ	skin:	n/a	n/a
4	CTCF	chr19:42075966-42077981	A549	lung:	n/a	chr19:42076414-42076427 chr19:42077151-42077172 chr19:42077156-42077174 chr19:42076411-42076424 chr19:42076411-42076429 chr19:42077158-42077171 chr19:42077157-42077173 chr19:42077014-42077027 chr19:42076311-42076324 chr19:42077161-42077169

No.	Distal block	Cell Line	Cell type
1	chr19:41954976..41956003-chr19:42076182..42077940,10	MCF-7	breast:
2	chr19:41877183..41879193-chr19:42077275..42079730,2	MCF-7	breast:
3	chr19:42048109..42049006-chr19:42076514..42077838,6	MCF-7	breast:
4	chr19:41953484..41955550-chr19:42076712..42078351,2	MCF-7	breast:

Variant related genes	Relation type
CEACAM21	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10153482	0.89[ASN][1000 genomes]
rs10405039	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10406221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409976	0.80[ASN][1000 genomes]
rs10415465	0.80[ASN][1000 genomes]
rs10415860	0.80[ASN][1000 genomes]
rs10420992	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10421574	0.90[ASN][1000 genomes]
rs11083627	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083629	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11673075	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150975	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462194	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983999	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1860255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2005606	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2191019	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302188	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2317314	0.90[ASN][1000 genomes]
rs34054275	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803479	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803481	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs714106	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257565	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs873910	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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	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	nsv962986	chr19:42073874-42080172	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11083628	AC011526.1	cis	Adipose Subcutaneous	GTEx
rs11083628	CEACAM21	cis	Whole Blood	GTEx
rs11083628	CEACAM21	cis	lung	GTEx
rs11083628	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs11083628	CEACAMP3	cis	lung	GTEx
rs11083628	CEACAM21	cis	Thyroid	GTEx
rs11083628	CEACAMP3	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42071600-42082000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr19:42072800-42078600	Weak transcription	Primary B cells from cord blood	blood
3	chr19:42076800-42081800	Weak transcription	GM12878-XiMat	blood
4	chr19:42077200-42079000	Weak transcription	Primary T cells from cord blood	blood
5	chr19:42077200-42081800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:42077200-42082000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:42077400-42078600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:42077400-42079000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:42077400-42080200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr19:42077400-42081600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:42077400-42081800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr19:42077400-42081800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:42077400-42082000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr19:42077400-42082000	Weak transcription	Lung	lung
15	chr19:42077600-42078200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:42077600-42078600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:42077600-42078800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:42077600-42081800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:42077600-42082000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:42077600-42082000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:42077800-42078200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr19:42077800-42080200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr19:42077800-42081200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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