Variant report

Variant	rs2317314
Chromosome Location	chr19:42062307-42062308
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	chr19:42055107..42057086-chr19:42062207..42064223,3	K562	blood:
2	chr19:42055153..42057086-chr19:42062207..42063970,2	K562	blood:

Variant related genes	Relation type
ENSG00000007129	Chromatin interaction
ENSG00000268027	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10153482	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405039	0.86[ASN][1000 genomes]
rs10406221	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs10420992	0.95[ASN][1000 genomes]
rs10421574	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424376	0.80[JPT][hapmap]
rs11083627	0.95[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs11083628	0.90[ASN][1000 genomes]
rs11668699	0.81[CHD][hapmap]
rs11673075	0.88[ASN][1000 genomes]
rs12150975	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12462194	0.90[ASN][1000 genomes]
rs12462897	0.81[CHD][hapmap]
rs12983999	0.95[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs1860255	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs2191019	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs2302188	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs34054275	0.82[ASN][1000 genomes]
rs3745936	0.86[CHB][hapmap]
rs3826716	0.81[CHD][hapmap]
rs4802122	0.85[CHD][hapmap]
rs4803479	0.94[ASN][1000 genomes]
rs4803481	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs714106	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs7255742	0.88[CHD][hapmap]
rs7257565	0.95[ASN][1000 genomes]
rs873910	0.82[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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs2317314	CEACAM21	cis	multi-tissue	Pritchard
rs2317314	KCNN4	cis	cerebellum	SCAN
rs2317314	CNFN	cis	multi-tissue	Pritchard
rs2317314	NUMBL	cis	multi-tissue	Pritchard
rs2317314	UBA6	cis	Liver	GTEx
rs2317314	CEACAM21	cis	Lymphoblastoid	GTEx
rs2317314	R29124_1	cis	multi-tissue	Pritchard
rs2317314	CEACAMP3	cis	lung	GTEx
rs2317314	CNFN	cis	cerebellum	SCAN
rs2317314	CEACAM21	cis	lymphoblastoid	seeQTL
rs2317314	LST1	cis	Liver	GTEx
rs2317314	CEACAMP3	cis	Whole Blood	GTEx
rs2317314	DHDH	cis	cerebellum	SCAN
rs2317314	ZNF234	cis	parietal	SCAN
rs2317314	GIPR	cis	parietal	SCAN
rs2317314	CEACAM21	cis	Whole Blood	GTEx
rs2317314	SCAF1	cis	parietal	SCAN
rs2317314	LST1	trans	multi-tissue	Pritchard
rs2317314	AF119839	trans	multi-tissue	Pritchard
rs2317314	MYPOP	cis	cerebellum	SCAN
rs2317314	CD3EAP	cis	parietal	SCAN
rs2317314	SPHK2	cis	cerebellum	SCAN
rs2317314	CEACAM4	cis	multi-tissue	Pritchard
rs2317314	RAB4B	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42058000-42069600	Weak transcription	Pancreas	Pancrea
2	chr19:42059200-42063200	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr19:42059800-42064600	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr19:42060600-42062600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:42060800-42063800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:42061000-42062400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr19:42061000-42062800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:42061200-42062600	Enhancers	Thymus	Thymus
9	chr19:42061400-42062400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr19:42061400-42062400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:42061400-42062600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr19:42061400-42062600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:42061600-42062400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:42061600-42062600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr19:42061600-42062600	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr19:42061600-42063200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr19:42061800-42062400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
18	chr19:42061800-42062400	Enhancers	Adipose Nuclei	Adipose
19	chr19:42061800-42062600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr19:42061800-42063200	Enhancers	Fetal Thymus	thymus
21	chr19:42061800-42065000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:42062000-42062400	Bivalent Enhancer	Left Ventricle	heart
23	chr19:42062000-42062400	Enhancers	Spleen	Spleen
24	chr19:42062000-42062600	Enhancers	Small Intestine	intestine
25	chr19:42062200-42062400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:42062200-42062400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
27	chr19:42062200-42062400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
28	chr19:42062200-42062400	Flanking Active TSS	GM12878-XiMat	blood
29	chr19:42062200-42062600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
30	chr19:42062200-42062600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
31	chr19:42062200-42062600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:42062200-42062600	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
33	chr19:42062200-42070000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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