Variant report

Variant	rs12462194
Chromosome Location	chr19:42072289-42072290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41959542..41961581-chr19:42071875..42074732,2	K562	blood:
2	chr19:42071841..42072361-chr2:230045042..230045586,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10153482	0.89[ASN][1000 genomes]
rs10405039	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10406221	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409976	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs10415465	0.80[ASN][1000 genomes]
rs10415860	0.80[ASN][1000 genomes]
rs10420992	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10421574	0.90[ASN][1000 genomes]
rs10421584	0.87[JPT][hapmap]
rs10424376	0.90[JPT][hapmap]
rs11083627	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083629	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11673075	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150975	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12983999	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1860255	0.95[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2005606	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2191019	0.95[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302188	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2317314	0.86[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs34054275	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3745936	1.00[CHB][hapmap]
rs3745938	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4802122	0.85[JPT][hapmap]
rs4803479	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803481	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs714106	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247842	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7255742	0.91[JPT][hapmap]
rs7257565	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs758350	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs873910	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	nsv978751	chr19:42036596-42073874	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12462194	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs12462194	AC011526.1	cis	Adipose Subcutaneous	GTEx
rs12462194	CEACAM21	cis	lung	GTEx
rs12462194	R29124_1	cis	multi-tissue	Pritchard
rs12462194	CEACAMP3	cis	lung	GTEx
rs12462194	CEACAM21	cis	Whole Blood	GTEx
rs12462194	CEACAM21	cis	Lymphoblastoid	GTEx
rs12462194	CEACAMP3	cis	Whole Blood	GTEx
rs12462194	CEACAM21	cis	Thyroid	GTEx
rs12462194	CEACAM21	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42069400-42077600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr19:42069600-42072600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:42069600-42073000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:42071400-42072600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:42071400-42074600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:42071400-42076400	Weak transcription	GM12878-XiMat	blood
7	chr19:42071600-42072400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr19:42071600-42073000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:42071600-42076400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:42071600-42082000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:42071800-42073000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr19:42071800-42073600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:42072000-42072400	Enhancers	Primary B cells from peripheral blood	blood
14	chr19:42072000-42072600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr19:42072000-42072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr19:42072000-42073200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr19:42072000-42073200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:42072000-42074200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:42072000-42074200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr19:42072000-42075000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:42072200-42073000	Enhancers	Primary T cells from cord blood	blood

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