Variant report

Variant	rs758350
Chromosome Location	chr19:42085162-42085163
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	chr19:42077943..42079577-chr19:42084170..42086427,2	K562	blood:
2	chr19:42078682..42081058-chr19:42082951..42085705,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10406221	0.83[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap]
rs10409976	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10415465	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10415860	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10421584	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10421785	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083627	0.82[JPT][hapmap]
rs12150975	0.80[JPT][hapmap]
rs12709854	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12709855	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12983999	0.82[JPT][hapmap]
rs16975382	0.81[EUR][1000 genomes]
rs17724225	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302188	0.84[CHD][hapmap]
rs28433747	0.94[ASN][1000 genomes]
rs28709791	0.90[ASN][1000 genomes]
rs34007391	0.99[ASN][1000 genomes]
rs35834169	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745936	0.83[CHB][hapmap]
rs3745938	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4803481	0.82[JPT][hapmap]
rs57979746	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58163879	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60646575	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs714106	0.83[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs7247842	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7251994	0.91[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7257657	0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740591	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs758350	R29124_1	cis	multi-tissue	Pritchard
rs758350	CEACAM21	cis	lymphoblastoid	seeQTL
rs758350	CEACAM21	cis	multi-tissue	Pritchard
rs758350	C19orf54	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42082200-42085200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:42082800-42086600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr19:42082800-42086600	Weak transcription	Lung	lung
4	chr19:42083200-42085400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:42083200-42085800	Weak transcription	GM12878-XiMat	blood
6	chr19:42083200-42086600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr19:42083200-42086600	Weak transcription	Thymus	Thymus
8	chr19:42083600-42086600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:42083600-42087000	Strong transcription	Primary T cells from cord blood	blood
10	chr19:42083600-42087000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:42083600-42094000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:42083800-42086800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:42083800-42088600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr19:42083800-42088600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:42083800-42093600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:42084000-42086600	Weak transcription	Placenta	Placenta
17	chr19:42084000-42092000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:42084000-42094200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:42084200-42087000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:42084200-42087800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:42084200-42089400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:42084400-42085600	Weak transcription	Spleen	Spleen
23	chr19:42084400-42085800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr19:42084400-42087600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:42084800-42086800	Strong transcription	Primary B cells from cord blood	blood
26	chr19:42084800-42087200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr19:42085000-42085200	Genic enhancers	Primary hematopoietic stem cells	blood
28	chr19:42085000-42086600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr19:42085000-42087200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
30	chr19:42085000-42088200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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