Variant report

Variant	rs10420992
Chromosome Location	chr19:42064462-42064463
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10153482	0.94[ASN][1000 genomes]
rs10405039	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10406221	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10409976	0.87[JPT][hapmap]
rs10421574	0.95[ASN][1000 genomes]
rs10421584	0.87[JPT][hapmap]
rs10423808	0.83[ASN][1000 genomes]
rs10424376	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11083626	0.82[ASN][1000 genomes]
rs11083627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083628	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083629	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11673075	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462194	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12983999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860255	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2005606	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2191019	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302188	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317314	0.95[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs34054275	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3745936	0.91[CHB][hapmap]
rs3745938	0.86[JPT][hapmap]
rs4802120	0.83[ASN][1000 genomes]
rs4802122	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4803479	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803481	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714106	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247842	0.82[JPT][hapmap]
rs7255742	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7257282	0.82[ASN][1000 genomes]
rs7257565	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758350	0.82[JPT][hapmap]
rs873910	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	nsv911770	chr19:41962486-42066279	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	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
3	nsv911772	chr19:41985624-42066279	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10420992	CEACAMP3	cis	lung	GTEx
rs10420992	CEACAMP3	cis	Whole Blood	GTEx
rs10420992	CEACAM21	cis	multi-tissue	Pritchard
rs10420992	AC011526.1	cis	Adipose Subcutaneous	GTEx
rs10420992	R29124_1	cis	multi-tissue	Pritchard
rs10420992	CEACAM21	cis	lung	GTEx
rs10420992	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs10420992	CEACAM21	cis	Lymphoblastoid	GTEx
rs10420992	CEACAM21	cis	Whole Blood	GTEx
rs10420992	CEACAM21	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42058000-42069600	Weak transcription	Pancreas	Pancrea
2	chr19:42059800-42064600	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr19:42061800-42065000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:42062200-42070000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr19:42062400-42065000	Genic enhancers	Primary B cells from cord blood	blood
6	chr19:42062400-42069600	Weak transcription	Spleen	Spleen
7	chr19:42062600-42064600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr19:42062600-42064600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:42062600-42065000	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr19:42062600-42065000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr19:42062600-42067400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:42062600-42067600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:42062600-42069400	Weak transcription	Thymus	Thymus
14	chr19:42062600-42069400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr19:42062800-42066200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:42063200-42066600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:42063600-42066400	Genic enhancers	Primary T cells from cord blood	blood
18	chr19:42063600-42068200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:42063800-42065000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr19:42063800-42065400	Strong transcription	GM12878-XiMat	blood
21	chr19:42064000-42064600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:42064000-42068000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr19:42064000-42069000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:42064400-42065000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:42064400-42065400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr19:42064400-42065600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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