Variant report

Variant	rs1865108
Chromosome Location	chr19:44330853-44330854
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	MXI1	chr19:44330804-44332486	IMR90	lung:	n/a	n/a
2	SIX5	chr19:44330813-44331786	A549	lung:	n/a	chr19:44331411-44331420 chr19:44331409-44331423 chr19:44331413-44331422
3	MAX	chr19:44330749-44332187	A549	lung:	n/a	chr19:44331687-44331697

No.	Distal block	Cell Line	Cell type
1	chr19:44330249..44332710-chr19:44437495..44440338,2	MCF-7	breast:
2	chr19:44330466..44332260-chr19:44438054..44440025,2	K562	blood:
3	chr19:44257672..44259708-chr19:44329404..44331468,2	K562	blood:
4	chr19:44323198..44325701-chr19:44330167..44332994,2	K562	blood:

Variant related genes	Relation type
ZNF283	TF binding region
ENSG00000159871	Chromatin interaction
ENSG00000124459	Chromatin interaction
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs189445	1.00[ASW][hapmap];0.86[CEU][hapmap]
rs2195980	0.81[CEU][hapmap]
rs349026	0.86[CEU][hapmap]
rs349027	1.00[ASW][hapmap];0.86[CEU][hapmap]
rs349035	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs349036	1.00[ASW][hapmap];0.86[CEU][hapmap]
rs349037	0.81[CEU][hapmap]
rs349056	1.00[YRI][hapmap]
rs379758	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1865108	SAE1	cis	cerebellum	SCAN
rs1865108	PVR	cis	parietal	SCAN
rs1865108	CEACAM19	cis	cerebellum	SCAN
rs1865108	IL1R2	trans	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44325000-44331000	Weak transcription	Aorta	Aorta
2	chr19:44325000-44331000	Weak transcription	Spleen	Spleen
3	chr19:44325200-44331000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:44325400-44331000	Weak transcription	HMEC	breast
5	chr19:44330200-44331000	Enhancers	Lung	lung
6	chr19:44330200-44331000	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr19:44330400-44332000	Active TSS	Fetal Brain Female	brain
8	chr19:44330600-44332200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr19:44330800-44331000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr19:44330800-44331000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr19:44330800-44331000	Enhancers	Primary B cells from peripheral blood	blood
12	chr19:44330800-44331000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr19:44330800-44331000	Active TSS	Primary hematopoietic stem cells	blood
14	chr19:44330800-44331000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:44330800-44331000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr19:44330800-44331000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:44330800-44331000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr19:44330800-44331000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:44330800-44331000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr19:44330800-44331000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:44330800-44331000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:44330800-44331000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:44330800-44331000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:44330800-44331000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:44330800-44331000	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr19:44330800-44331000	Enhancers	Duodenum Mucosa	Duodenum
27	chr19:44330800-44331000	Enhancers	Ovary	ovary
28	chr19:44330800-44331000	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:44330800-44331000	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr19:44330800-44331000	Enhancers	Dnd41	blood
31	chr19:44330800-44331000	Enhancers	NHEK	skin
32	chr19:44330800-44331200	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr19:44330800-44331200	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr19:44330800-44331200	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr19:44330800-44331200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr19:44330800-44331200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:44330800-44331200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr19:44330800-44331200	Flanking Active TSS	Fetal Brain Male	brain
39	chr19:44330800-44331200	Flanking Active TSS	GM12878-XiMat	blood
40	chr19:44330800-44331400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:44330800-44331400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
42	chr19:44330800-44331400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr19:44330800-44331400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr19:44330800-44331400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr19:44330800-44331400	Active TSS	Right Atrium	heart
46	chr19:44330800-44331800	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr19:44330800-44331800	Active TSS	Colon Smooth Muscle	Colon
48	chr19:44330800-44332000	Active TSS	Primary T cells from cord blood	blood
49	chr19:44330800-44332000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr19:44330800-44332000	Active TSS	Stomach Smooth Muscle	stomach

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