Variant report

Variant	rs12782
Chromosome Location	chr5:115152249-115152250
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	CTCF	chr5:115152100-115152250	HepG2	liver:	n/a	n/a
2	REST	chr5:115151061-115153120	H1-neurons	neurons:	n/a	chr5:115152626-115152639
3	E2F6	chr5:115151447-115152881	H1-hESC	embryonic stem cell:	n/a	chr5:115151891-115151901 chr5:115152461-115152470
4	CHD2	chr5:115151997-115152705	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:115152084-115152746	SK-N-MC	brain:	n/a	n/a
6	SIN3AK20	chr5:115152025-115152292	SK-N-SH	brain:	n/a	n/a
7	CREB1	chr5:115151688-115152885	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:115152129-115152437	HepG2	liver:	n/a	n/a
9	USF2	chr5:115152188-115152391	H1-hESC	embryonic stem cell:	n/a	n/a
10	CHD1	chr5:115152141-115152996	IMR90	lung:	n/a	n/a
11	TAF7	chr5:115151989-115152833	H1-hESC	embryonic stem cell:	n/a	n/a
12	HEY1	chr5:115152060-115152846	HepG2	liver:	n/a	n/a
13	HEY1	chr5:115152168-115152472	HepG2	liver:	n/a	n/a
14	RCOR1	chr5:115151841-115152611	HepG2	liver:	n/a	n/a
15	POLR2A	chr5:115152019-115152848	SK-N-MC	brain:	n/a	n/a
16	TAF1	chr5:115151897-115152873	H1-neurons	neurons:	n/a	n/a
17	JUND	chr5:115151296-115152876	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr5:115151132-115152960	H1-neurons	neurons:	n/a	n/a
19	RFX5	chr5:115152127-115152327	HepG2	liver:	n/a	n/a
20	TAF7	chr5:115152132-115152693	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr5:115152160-115152410	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr5:115151975-115152804	H1-hESC	embryonic stem cell:	n/a	n/a
23	EGR1	chr5:115152214-115152664	H1-hESC	embryonic stem cell:	n/a	chr5:115152456-115152469 chr5:115152457-115152468 chr5:115152510-115152520
24	MAZ	chr5:115152155-115152536	HepG2	liver:	n/a	n/a
25	JUND	chr5:115151780-115152752	H1-hESC	embryonic stem cell:	n/a	n/a
26	GTF2F1	chr5:115151962-115152661	H1-hESC	embryonic stem cell:	n/a	n/a
27	YY1	chr5:115151599-115152915	H1-hESC	embryonic stem cell:	n/a	chr5:115151779-115151790 chr5:115152458-115152467 chr5:115151884-115151898 chr5:115151889-115151898
28	ZNF143	chr5:115152141-115152737	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr5:115151796-115152846	H1-hESC	embryonic stem cell:	n/a	chr5:115152458-115152467 chr5:115151884-115151898 chr5:115151889-115151898
30	EP300	chr5:115152206-115152767	H1-hESC	embryonic stem cell:	n/a	chr5:115152721-115152735
31	POLR2A	chr5:115152213-115152367	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr5:115152167-115152444	MCF10A-Er-Src	breast:	n/a	n/a
33	TAF1	chr5:115152021-115152880	H1-hESC	embryonic stem cell:	n/a	n/a
34	ZNF263	chr5:115150963-115152852	HEK293-T-REx	kidney:	n/a	n/a
35	POLR2A	chr5:115152037-115152441	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr5:115152027-115152844	HepG2	liver:	n/a	n/a
37	POLR2A	chr5:115152135-115152697	IMR90	lung:	n/a	n/a
38	POLR2A	chr5:115151190-115152887	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr5:115151822-115152891	HepG2	liver:	n/a	n/a
40	POLR2A	chr5:115152157-115152710	HepG2	liver:	n/a	n/a
41	POLR2A	chr5:115151205-115152841	H1-hESC	embryonic stem cell:	n/a	n/a
42	BHLHE40	chr5:115151693-115152773	HepG2	liver:	n/a	n/a
43	POLR2A	chr5:115152051-115152538	HepG2	liver:	n/a	n/a
44	POLR2A	chr5:115151741-115152866	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr5:115152078-115152486	SK-N-SH	brain:	n/a	n/a
46	TAF1	chr5:115151486-115152833	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr5:115151831-115152733	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr5:115151989-115152775	H1-neurons	neurons:	n/a	chr5:115152626-115152639
49	POLR2A	chr5:115152132-115152392	HepG2	liver:	n/a	n/a
50	SIN3AK20	chr5:115151985-115152254	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115147173..115150653-chr5:115151450..115154733,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-1	chr5:115151929-115152868	NONHSAT103327

Variant related genes	Relation type
CDO1	TF binding region
ENSG00000129596	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10058994	0.88[AMR][1000 genomes]
rs10477545	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10478261	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes]
rs10519429	1.00[MEX][hapmap];0.88[AMR][1000 genomes]
rs11241338	1.00[MEX][hapmap]
rs11951965	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11958544	0.83[AMR][1000 genomes]
rs11959754	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11960070	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1968365	0.88[AMR][1000 genomes]
rs4920894	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60326315	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594908	1.00[CEU][hapmap];0.82[LWK][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6865002	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73259615	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73265491	0.88[AMR][1000 genomes]
rs73267415	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73780662	0.86[EUR][1000 genomes]
rs9326975	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115149200-115152800	Active TSS	Aorta	Aorta
2	chr5:115149800-115153000	Active TSS	Liver	Liver
3	chr5:115150200-115152600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:115150600-115153000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:115150800-115152400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr5:115150800-115152600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr5:115150800-115152800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:115150800-115152800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:115150800-115152800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:115150800-115153400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr5:115151000-115152400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
12	chr5:115151000-115152600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:115151000-115152800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr5:115151000-115152800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr5:115151000-115152800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:115151000-115152800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:115151000-115152800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
18	chr5:115151000-115153000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:115151000-115153200	Active TSS	Fetal Brain Male	brain
20	chr5:115151000-115153200	Active TSS	Fetal Brain Female	brain
21	chr5:115151000-115153200	Active TSS	Fetal Kidney	kidney
22	chr5:115151200-115152600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:115151200-115152600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr5:115151200-115152600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
25	chr5:115151200-115152800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:115151200-115152800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:115151200-115152800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr5:115151200-115153000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr5:115151200-115153000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr5:115151200-115153000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr5:115151200-115153000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr5:115151200-115153200	Active TSS	Brain Germinal Matrix	brain
33	chr5:115151200-115153200	Bivalent/Poised TSS	Fetal Lung	lung
34	chr5:115151400-115152400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
35	chr5:115151400-115152600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:115151400-115152600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
37	chr5:115151400-115152600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
38	chr5:115151400-115152600	Bivalent/Poised TSS	NHLF	lung
39	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:115151400-115152800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:115151400-115152800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr5:115151400-115152800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:115151400-115152800	Active TSS	Brain Angular Gyrus	brain
46	chr5:115151400-115152800	Active TSS	Brain Hippocampus Middle	brain
47	chr5:115151400-115152800	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr5:115151400-115152800	Active TSS	Brain Substantia Nigra	brain
49	chr5:115151400-115152800	Flanking Active TSS	Lung	lung
50	chr5:115151400-115152800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum

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