Variant report

Variant	rs16878144
Chromosome Location	chr5:59783541-59783542
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	EP300	chr5:59783394-59784088	SK-N-SH_RA	brain:	n/a	n/a
2	FOSL2	chr5:59783149-59783918	A549	lung:	n/a	chr5:59783429-59783440
3	GATA3	chr5:59783002-59783888	A549	lung:	n/a	chr5:59783322-59783330
4	HNF4A	chr5:59783230-59783594	HepG2	liver:	n/a	chr5:59783371-59783379
5	POLR2A	chr5:59783352-59784232	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:59783447-59783658	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:59783210-59784179	HepG2	liver:	n/a	n/a
8	FOXA1	chr5:59783137-59784225	HepG2	liver:	n/a	chr5:59783513-59783525
9	MYBL2	chr5:59783197-59783738	HepG2	liver:	n/a	n/a
10	HDAC2	chr5:59783245-59783742	HepG2	liver:	n/a	n/a
11	TCF12	chr5:59783167-59783927	A549	lung:	n/a	n/a
12	NFIC	chr5:59783186-59783943	HepG2	liver:	n/a	n/a
13	FOXA1	chr5:59783207-59783766	HepG2	liver:	n/a	chr5:59783513-59783525
14	RXRA	chr5:59783320-59783682	HepG2	liver:	n/a	n/a
15	JUND	chr5:59783297-59783668	A549	lung:	n/a	chr5:59783429-59783440
16	EP300	chr5:59783344-59784203	HepG2	liver:	n/a	n/a
17	RCOR1	chr5:59783068-59783794	HepG2	liver:	n/a	n/a
18	MAFF	chr5:59783400-59784198	HepG2	liver:	n/a	chr5:59783782-59783800
19	SP1	chr5:59783195-59783957	A549	lung:	n/a	n/a
20	PBX3	chr5:59783417-59783827	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr5:59783385-59784320	HepG2	liver:	n/a	n/a
22	BCL3	chr5:59783314-59783823	A549	lung:	n/a	n/a
23	HEY1	chr5:59783204-59784375	HepG2	liver:	n/a	n/a
24	YY1	chr5:59783378-59783661	HepG2	liver:	n/a	n/a
25	FOXA2	chr5:59783112-59784133	HepG2	liver:	n/a	chr5:59783513-59783525
26	RAD21	chr5:59783293-59783722	HepG2	liver:	n/a	n/a
27	EP300	chr5:59783376-59784114	SK-N-SH_RA	brain:	n/a	n/a
28	EP300	chr5:59783123-59783887	A549	lung:	n/a	n/a
29	HEY1	chr5:59783454-59783715	HepG2	liver:	n/a	n/a
30	MAX	chr5:59783304-59784177	A549	lung:	n/a	n/a
31	HNF4A	chr5:59783264-59783620	HepG2	liver:	n/a	chr5:59783371-59783379
32	MYBL2	chr5:59783185-59783922	HepG2	liver:	n/a	n/a
33	FOXA1	chr5:59783186-59783748	HepG2	liver:	n/a	chr5:59783513-59783525
34	NFIC	chr5:59783207-59783700	HepG2	liver:	n/a	n/a
35	MXI1	chr5:59782832-59784903	SK-N-SH	brain:	n/a	n/a
36	REST	chr5:59783209-59783733	A549	lung:	n/a	n/a
37	EP300	chr5:59783185-59783723	HepG2	liver:	n/a	n/a
38	FOXA2	chr5:59783290-59783669	A549	lung:	n/a	chr5:59783513-59783525
39	FOXA1	chr5:59783294-59783760	HepG2	liver:	n/a	chr5:59783513-59783525
40	HDAC2	chr5:59783207-59783614	HepG2	liver:	n/a	n/a
41	HNF4G	chr5:59783259-59783655	HepG2	liver:	n/a	chr5:59783371-59783379
42	MBD4	chr5:59783249-59784105	HepG2	liver:	n/a	n/a
43	FOSL2	chr5:59783250-59783724	A549	lung:	n/a	chr5:59783429-59783440
44	FOXA2	chr5:59783252-59783811	A549	lung:	n/a	chr5:59783513-59783525
45	EP300	chr5:59782537-59784681	SK-N-SH	brain:	n/a	chr5:59782848-59782858
46	TBP	chr5:59783372-59784241	HepG2	liver:	n/a	n/a
47	TCF7L2	chr5:59783017-59783717	HepG2	liver:	n/a	n/a
48	POLR2A	chr5:59783358-59784321	HepG2	liver:	n/a	n/a
49	EP300	chr5:59783218-59783808	A549	lung:	n/a	n/a
50	EP300	chr5:59783173-59783694	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC109486.1-1	chr5:59783540-59784250	ENSG00000152931
2	lnc-AC109486.1-1	chr5:59783540-59784250	NONHSAT101637
3	lnc-AC109486.1-1	chr5:59783540-59784250	ENSG00000152931.7

Variant related genes	Relation type
PART1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10045433	1.00[CHD][hapmap]
rs10516154	0.80[EUR][1000 genomes]
rs10939840	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs10939842	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs10939849	0.83[EUR][1000 genomes]
rs11740770	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11746901	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11948687	0.93[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12153271	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs12153798	0.87[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12188950	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16877912	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs28481826	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2898278	0.82[CEU][hapmap]
rs6449470	1.00[CHD][hapmap]
rs7719095	0.93[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16878144	PDE4D	cis	cerebellum	SCAN
rs16878144	CTSH	trans	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59767200-59789000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59781400-59786600	Active TSS	Aorta	Aorta
3	chr5:59782000-59801000	Weak transcription	Fetal Brain Male	brain
4	chr5:59782400-59783600	Enhancers	Stomach Mucosa	stomach
5	chr5:59782400-59787200	Active TSS	Stomach Smooth Muscle	stomach
6	chr5:59782800-59784000	Flanking Active TSS	HepG2	liver
7	chr5:59782800-59785000	Active TSS	Brain Cingulate Gyrus	brain
8	chr5:59782800-59786000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:59783000-59783600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:59783000-59783600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
11	chr5:59783000-59783800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:59783000-59783800	Enhancers	Colon Smooth Muscle	Colon
13	chr5:59783000-59783800	Enhancers	Fetal Lung	lung
14	chr5:59783000-59783800	Enhancers	HMEC	breast
15	chr5:59783000-59784000	Enhancers	Brain Hippocampus Middle	brain
16	chr5:59783000-59784000	Enhancers	Fetal Brain Female	brain
17	chr5:59783000-59784200	Enhancers	Brain Anterior Caudate	brain
18	chr5:59783000-59785600	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr5:59783000-59787600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr5:59783200-59783600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:59783200-59783600	Enhancers	NHLF	lung
22	chr5:59783200-59783800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:59783200-59783800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:59783200-59783800	Enhancers	Fetal Kidney	kidney
25	chr5:59783200-59784800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:59783400-59783600	Enhancers	Duodenum Mucosa	Duodenum
27	chr5:59783400-59783600	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr5:59783400-59783600	Enhancers	NHDF-Ad	bronchial
29	chr5:59783400-59783800	Enhancers	Fetal Stomach	stomach
30	chr5:59783400-59783800	Enhancers	NHEK	skin
31	chr5:59783400-59783800	Enhancers	Osteobl	bone
32	chr5:59783400-59784000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr5:59783400-59784200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:59783400-59784600	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr5:59783400-59785000	Active TSS	Brain Angular Gyrus	brain
36	chr5:59783400-59785000	Enhancers	HSMM	muscle
37	chr5:59783400-59785400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr5:59783400-59785400	Flanking Active TSS	A549	lung

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