Variant report

Variant	rs888817
Chromosome Location	chr5:80257798-80257799
allele	C/T
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	POLR2A	chr5:80257738-80258119	SK-N-MC	brain:	n/a	n/a
2	CEBPB	chr5:80257643-80257958	IMR90	lung:	n/a	n/a
3	MXI1	chr5:80257755-80257834	HepG2	liver:	n/a	n/a
4	RCOR1	chr5:80257637-80257832	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:80257697-80257993	HepG2	liver:	n/a	n/a
6	CEBPB	chr5:80257653-80257965	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:80257690-80257958	HepG2	liver:	n/a	n/a
8	CEBPB	chr5:80257649-80257909	A549	lung:	n/a	n/a
9	POLR2A	chr5:80257661-80257986	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80257641..80260093-chr5:80260267..80261887,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251450	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13357015	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73123076	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3330937	chr5:80255346-80257994	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3359411	chr5:80255421-80257969	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs888817	LOC644936	cis	parietal	SCAN
rs888817	AP3B1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80255600-80258000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr5:80255600-80258000	Active TSS	Ovary	ovary
3	chr5:80255800-80258000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr5:80255800-80258000	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr5:80255800-80258000	Active TSS	Brain Anterior Caudate	brain
6	chr5:80255800-80258000	Bivalent/Poised TSS	Psoas Muscle	Psoas
7	chr5:80255800-80258200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:80255800-80258200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr5:80255800-80258200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:80255800-80258200	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr5:80255800-80259000	Active TSS	NHLF	lung
12	chr5:80255800-80259600	Active TSS	Brain Substantia Nigra	brain
13	chr5:80255800-80261000	Active TSS	Right Atrium	heart
14	chr5:80255800-80261200	Active TSS	Brain Cingulate Gyrus	brain
15	chr5:80255800-80261600	Active TSS	Brain Angular Gyrus	brain
16	chr5:80256000-80257800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:80256000-80257800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:80256000-80257800	Bivalent/Poised TSS	NHDF-Ad	bronchial
19	chr5:80256000-80258000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:80256000-80258000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:80256000-80258000	Bivalent/Poised TSS	Left Ventricle	heart
22	chr5:80256000-80258000	Active TSS	Rectal Smooth Muscle	rectum
23	chr5:80256000-80258200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr5:80256000-80258400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr5:80256000-80258600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr5:80256000-80259200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr5:80256000-80261000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr5:80256000-80261400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:80256600-80257800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:80256800-80258000	Bivalent/Poised TSS	Fetal Kidney	kidney
31	chr5:80256800-80258000	Bivalent/Poised TSS	HepG2	liver
32	chr5:80257000-80257800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr5:80257000-80257800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
34	chr5:80257000-80257800	Bivalent/Poised TSS	Thymus	Thymus
35	chr5:80257000-80258000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:80257000-80258000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:80257000-80258000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
38	chr5:80257000-80258600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr5:80257200-80257800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr5:80257200-80257800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:80257200-80257800	Bivalent Enhancer	Fetal Lung	lung
42	chr5:80257200-80257800	Bivalent Enhancer	HUVEC	blood vessel
43	chr5:80257200-80258000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
44	chr5:80257200-80258000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr5:80257200-80258000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr5:80257200-80258000	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr5:80257200-80258000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:80257200-80258000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr5:80257200-80258000	Active TSS	Right Ventricle	heart
50	chr5:80257200-80258600	Active TSS	Primary T helper naive cells fromperipheralblood	blood

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