Variant report

Variant	rs7713216
Chromosome Location	chr5:111495381-111495382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr5:111495267-111495400	H1-hESC	embryonic stem cell:	n/a	chr5:111495341-111495354
2	CEBPB	chr5:111495188-111495512	K562	blood:	n/a	chr5:111495341-111495354

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:111495353-111495403	AG09309	skin:	n/a
2	chr5:111495353-111495403	NH-A	brain:	n/a
3	chr5:111495353-111495403	NHDF-neo	bronchial:	n/a
4	chr5:111495353-111495403	HRCEpiC	kidney:	n/a
5	chr5:111495353-111495403	BE2_C	brain:	n/a
6	chr5:111495353-111495403	Caco-2	colon:	n/a
7	chr5:111495353-111495403	A549	lung:	n/a
8	chr5:111495353-111495403	Jurkat	blood:	n/a
9	chr5:111495353-111495403	ECC-1	luminal epithelium:	n/a
10	chr5:111495353-111495403	HL-60	blood:	n/a
11	chr5:111495353-111495403	HPAEpiC	pulmonary alveolar:	n/a
12	chr5:111495353-111495403	PFSK-1	brain:	n/a
13	chr5:111495353-111495403	NB4	blood:	n/a
14	chr5:111495353-111495403	AoSMC	blood vessel:	n/a
15	chr5:111495353-111495403	HCPEpiC	choroid plexus:	n/a
16	chr5:111495353-111495403	HMEC	breast:	n/a
17	chr5:111495353-111495403	HCM	heart:	n/a
18	chr5:111495353-111495403	SKMC	muscle:	n/a
19	chr5:111495353-111495403	GM12891	blood:	n/a
20	chr5:111495353-111495403	BJ	skin:	n/a
21	chr5:111495353-111495403	HUVEC	blood vessel:	n/a
22	chr5:111495353-111495403	IMR90	lung:	fetal
23	chr5:111495353-111495403	GM06990	blood:	n/a
24	chr5:111495353-111495403	GM12892	blood:	n/a
25	chr5:111495353-111495403	SK-N-MC	brain:	n/a
26	chr5:111495353-111495403	HRE	kidney:	n/a
27	chr5:111495353-111495403	NT2-D1	testis:	n/a
28	chr5:111495353-111495403	CMK	blood:	n/a
29	chr5:111495353-111495403	LNCaP	prostate:	n/a
30	chr5:111495353-111495403	HEEpiC	esophagus:	n/a
31	chr5:111495353-111495403	AG04450	lung:	fetal
32	chr5:111495353-111495403	GM19239	blood:	n/a
33	chr5:111495353-111495403	HCT-116	colon:	n/a
34	chr5:111495353-111495403	GM12878	blood:	n/a
35	chr5:111495353-111495403	AG09319	gingival:	n/a
36	chr5:111495353-111495403	HepG2	liver:	n/a
37	chr5:111495353-111495403	ProgFib	skin:	n/a
38	chr5:111495353-111495403	NHBE	bronchial:	n/a
39	chr5:111495353-111495403	K562	blood:	n/a
40	chr5:111495353-111495403	MCF10A-Er-Src	breast:	n/a
41	chr5:111495353-111495403	SK-N-SH	brain:	n/a
42	chr5:111495353-111495403	HNPCEpiC	eye:	n/a
43	chr5:111495353-111495403	HAEpiC	amniotic membrane:	n/a
44	chr5:111495353-111495403	HRPEpiC	eye:	n/a
45	chr5:111495353-111495403	U87	brain:	n/a
46	chr5:111495353-111495403	SAEC	small airway:	n/a
47	chr5:111495353-111495403	Hela-S3	cervix:	n/a
48	chr5:111495353-111495403	RPTEC	kidney:	n/a
49	chr5:111495353-111495403	HEK293	kidney:	embryo
50	chr5:111495353-111495403	T-47D	breast:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:110427977..110430088-chr5:111495107..111498582,4	K562	blood:
2	chr1:149858447..149860137-chr5:111495190..111496894,2	MCF-7	breast:
3	chr5:111495302..111497808-chr5:111754204..111756858,3	MCF-7	breast:
4	chr5:110848137..110849903-chr5:111495270..111497479,2	MCF-7	breast:
5	chr5:111091669..111093632-chr5:111494994..111496527,2	MCF-7	breast:
6	chr5:110846086..110848469-chr5:111495331..111498521,3	K562	blood:

No data

Variant related genes	Relation type
SNORA13	TF binding region
EPB41L4A-AS1	TF binding region
EPB41L4A-AS1	CpG island
SNORA13	CpG island
ENSG00000184270	Chromatin interaction
ENSG00000246859	Chromatin interaction
ENSG00000134987	Chromatin interaction
ENSG00000268358	Chromatin interaction
ENSG00000134986	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000164211	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000129595	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10045569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1078129	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs12517400	0.83[GIH][hapmap]
rs13165611	0.89[CHB][hapmap]
rs17134155	0.85[CEU][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs17134162	0.88[ASN][1000 genomes]
rs17134228	0.89[CHB][hapmap]
rs17134250	0.89[CHB][hapmap]
rs17265886	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs1863960	0.89[CHB][hapmap]
rs2162733	0.89[CHB][hapmap]
rs2290990	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303657	0.88[CHB][hapmap]
rs2900059	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2900060	0.90[EUR][1000 genomes]
rs3797320	0.89[CHB][hapmap]
rs3816657	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs55812441	0.90[EUR][1000 genomes]
rs56158171	0.96[EUR][1000 genomes]
rs61482608	0.96[EUR][1000 genomes]
rs6873159	0.89[CHB][hapmap]
rs73787781	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7449256	0.96[EUR][1000 genomes]
rs7700705	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7711555	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs7720064	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs7720344	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7730625	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7713216	PJA2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111489000-111496000	Weak transcription	Gastric	stomach
2	chr5:111491200-111496000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:111491200-111496200	Weak transcription	Aorta	Aorta
4	chr5:111491400-111495800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr5:111491400-111496000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:111491600-111496000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:111492400-111496200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:111492400-111496200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:111492600-111496000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:111493600-111496000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:111494200-111496000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:111494200-111496400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:111494400-111496000	Enhancers	Fetal Lung	lung
14	chr5:111494600-111496000	Enhancers	NHDF-Ad	bronchial
15	chr5:111494800-111496000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:111495000-111495400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:111495200-111495800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr5:111495200-111496000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:111495200-111496000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:111495200-111496000	Enhancers	Fetal Heart	heart
21	chr5:111495200-111496000	Enhancers	Placenta	Placenta
22	chr5:111495200-111496000	Enhancers	Left Ventricle	heart
23	chr5:111495200-111496200	Enhancers	Right Ventricle	heart

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