Variant report

Variant	rs4288343
Chromosome Location	chr8:99305539-99305540
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24719766..24721631-chr8:99304778..99307612,2	MCF-7	breast:
2	chr8:95651216..95652910-chr8:99304920..99307461,2	MCF-7	breast:
3	chr2:86421327..86423660-chr8:99303877..99305553,2	MCF-7	breast:
4	chr8:99268498..99270125-chr8:99304493..99306016,2	MCF-7	breast:
5	chr8:99266294..99268249-chr8:99305433..99307936,2	MCF-7	breast:
6	chr8:99304071..99306084-chr8:99410525..99412832,2	MCF-7	breast:
7	chr6:26204334..26206803-chr8:99304596..99307549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104361	Chromatin interaction
ENSG00000261437	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000273080	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7461545	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv831406	chr8:99290745-99482076	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4288343	NPAL2	cis	multi-tissue	Pritchard
rs4288343	NPAL2	Cis_1M	lymphoblastoid	RTeQTL
rs4288343	NA	cis	multi-tissue	Pritchard
rs4288343	NIPAL2	cis	multi-tissue	Pritchard
rs4288343	NIPAL2	cis	Whole Blood	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99296400-99305600	Weak transcription	Left Ventricle	heart
2	chr8:99296400-99305600	Weak transcription	Lung	lung
3	chr8:99296400-99305600	Weak transcription	Pancreas	Pancrea
4	chr8:99304200-99307400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr8:99304600-99305800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:99304600-99306000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr8:99304600-99306600	Active TSS	GM12878-XiMat	blood
8	chr8:99304600-99307400	Active TSS	Brain Anterior Caudate	brain
9	chr8:99304800-99305600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:99304800-99306400	Active TSS	NHLF	lung
11	chr8:99304800-99306800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr8:99304800-99306800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:99304800-99306800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr8:99304800-99307000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr8:99304800-99312400	Weak transcription	K562	blood
16	chr8:99305000-99305800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:99305000-99306200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr8:99305000-99306200	Flanking Active TSS	HUVEC	blood vessel
19	chr8:99305000-99306600	Active TSS	HMEC	breast
20	chr8:99305000-99306600	Active TSS	NHDF-Ad	bronchial
21	chr8:99305200-99305600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr8:99305200-99305800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr8:99305200-99305800	Flanking Active TSS	Osteobl	bone
24	chr8:99305200-99306000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr8:99305200-99306200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr8:99305200-99306200	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr8:99305200-99306600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr8:99305200-99306600	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr8:99305200-99306600	Active TSS	Stomach Smooth Muscle	stomach
30	chr8:99305200-99306800	Active TSS	Fetal Stomach	stomach
31	chr8:99305200-99306800	Active TSS	NHEK	skin
32	chr8:99305200-99307000	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr8:99305200-99307000	Active TSS	Fetal Intestine Large	intestine
34	chr8:99305400-99305600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
35	chr8:99305400-99305600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr8:99305400-99305600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
37	chr8:99305400-99305600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
38	chr8:99305400-99305600	Active TSS	Primary T cells from cord blood	blood
39	chr8:99305400-99305600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr8:99305400-99305600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:99305400-99305600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr8:99305400-99305600	Flanking Active TSS	Fetal Lung	lung
43	chr8:99305400-99305600	Bivalent/Poised TSS	Fetal Thymus	thymus
44	chr8:99305400-99305600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr8:99305400-99305600	Active TSS	NH-A	brain
46	chr8:99305400-99305800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
47	chr8:99305400-99305800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr8:99305400-99305800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr8:99305400-99305800	Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr8:99305400-99305800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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