Variant report

Variant	rs1560723
Chromosome Location	chr19:51400356-51400357
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	chr19:51400331-51400577	GM12878	blood:	n/a	n/a
2	USF2	chr19:51399820-51401101	GM12878	blood:	n/a	n/a
3	POU2F2	chr19:51399676-51400538	GM12891	blood:	n/a	n/a
4	RELA	chr19:51399813-51401112	GM18526	blood:	n/a	n/a
5	JUND	chr19:51399864-51400380	K562	blood:	n/a	chr19:51400073-51400083 chr19:51400073-51400083 chr19:51400072-51400084 chr19:51400073-51400083 chr19:51400072-51400083 chr19:51400031-51400040 chr19:51400073-51400082
6	MEF2A	chr19:51399716-51400472	GM12878	blood:	n/a	chr19:51400074-51400082
7	TBP	chr19:51399741-51400985	GM12878	blood:	n/a	n/a
8	CEBPB	chr19:51399685-51400979	GM12878	blood:	n/a	n/a
9	KAP1	chr19:51399852-51400365	HEK293	kidney:	n/a	n/a
10	MXI1	chr19:51399745-51401061	GM12878	blood:	n/a	n/a
11	EP300	chr19:51399783-51401081	GM12878	blood:	n/a	chr19:51400074-51400083
12	FOXM1	chr19:51399719-51400928	GM12878	blood:	n/a	n/a
13	MAX	chr19:51399793-51400400	HCT-116	colon:	n/a	chr19:51399997-51400008 chr19:51400109-51400120
14	RELA	chr19:51399839-51401122	GM19099	blood:	n/a	n/a
15	EBF1	chr19:51399732-51401194	GM12878	blood:	n/a	n/a
16	MTA3	chr19:51399720-51401135	GM12878	blood:	n/a	n/a
17	EP300	chr19:51399719-51401397	GM12878	blood:	n/a	chr19:51400074-51400083
18	MEF2C	chr19:51399824-51400791	GM12878	blood:	n/a	chr19:51400074-51400082
19	MAX	chr19:51399799-51401112	GM12878	blood:	n/a	chr19:51399997-51400008 chr19:51400109-51400120
20	ATF2	chr19:51399748-51400831	GM12878	blood:	n/a	n/a
21	RUNX3	chr19:51399667-51401253	GM12878	blood:	n/a	chr19:51400137-51400146
22	POU2F2	chr19:51399728-51400408	GM12891	blood:	n/a	n/a
23	PAX5	chr19:51399691-51400397	GM12878	blood:	n/a	chr19:51400035-51400052 chr19:51400036-51400054 chr19:51400035-51400054
24	USF1	chr19:51399739-51400400	HCT-116	colon:	n/a	n/a
25	SETDB1	chr19:51399719-51400418	U2OS	brain:	n/a	n/a
26	BATF	chr19:51399841-51400784	GM12878	blood:	n/a	n/a
27	USF1	chr19:51399766-51400405	HCT-116	colon:	n/a	n/a
28	FOXM1	chr19:51399672-51400874	GM12878	blood:	n/a	n/a
29	BCL3	chr19:51399741-51400491	GM12878	blood:	n/a	n/a
30	PAX5	chr19:51399770-51400357	GM12891	blood:	n/a	chr19:51400035-51400052 chr19:51400036-51400054 chr19:51400035-51400054
31	JUN	chr19:51399667-51400872	K562	blood:	n/a	chr19:51400073-51400083 chr19:51400073-51400083 chr19:51400072-51400084 chr19:51400073-51400083 chr19:51400031-51400040 chr19:51400030-51400043 chr19:51400073-51400082
32	SP1	chr19:51399735-51401140	GM12878	blood:	n/a	chr19:51400737-51400750
33	STAT5A	chr19:51399721-51400994	GM12878	blood:	n/a	chr19:51400073-51400082
34	SREBP2	chr19:51399463-51401377	GM12878	blood:	n/a	n/a
35	WRNIP1	chr19:51399791-51401549	GM12878	blood:	n/a	n/a
36	NFATC1	chr19:51399764-51400693	GM12878	blood:	n/a	n/a
37	NFIC	chr19:51399682-51400739	GM12878	blood:	n/a	n/a
38	TCF3	chr19:51399752-51401095	GM12878	blood:	n/a	n/a
39	MAX	chr19:51399767-51400464	HCT-116	colon:	n/a	chr19:51399997-51400008 chr19:51400109-51400120
40	STAT1	chr19:51399804-51400875	GM12878	blood:	n/a	chr19:51400073-51400082
41	STAT3	chr19:51399854-51400739	GM12878	blood:	n/a	chr19:51400073-51400082
42	JUND	chr19:51399790-51401173	GM12878	blood:	n/a	chr19:51400073-51400083 chr19:51400073-51400083 chr19:51400072-51400084 chr19:51400073-51400083 chr19:51400072-51400083 chr19:51400031-51400040 chr19:51400073-51400082
43	RELA	chr19:51399845-51401050	GM19193	blood:	n/a	n/a
44	RELA	chr19:51399702-51401142	GM12891	blood:	n/a	n/a
45	IRF4	chr19:51399751-51400636	GM12878	blood:	n/a	n/a
46	POU2F2	chr19:51399658-51401090	GM12878	blood:	n/a	n/a
47	CHD1	chr19:51399763-51401491	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:51399659-51400478	GM12891	blood:	n/a	n/a
49	MEF2A	chr19:51399847-51400418	GM12878	blood:	n/a	chr19:51400074-51400082
50	IKZF1	chr19:51399524-51401263	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:51400321-51400371	HL-60	blood:	n/a
2	chr19:51400352-51400402	SK-N-SH	brain:	n/a
3	chr19:51400321-51400371	HRE	kidney:	n/a
4	chr19:51400321-51400371	CMK	blood:	n/a
5	chr19:51400352-51400402	AG04449	skin:	fetal
6	chr19:51400352-51400402	IMR90	lung:	fetal
7	chr19:51400321-51400371	AoSMC	blood vessel:	n/a
8	chr19:51400321-51400371	NT2-D1	testis:	n/a
9	chr19:51400352-51400402	NHBE	bronchial:	n/a
10	chr19:51400352-51400402	GM06990	blood:	n/a
11	chr19:51400321-51400371	BJ	skin:	n/a
12	chr19:51400352-51400402	K562	blood:	n/a
13	chr19:51400321-51400371	T-47D	breast:	n/a
14	chr19:51400352-51400402	SK-N-MC	brain:	n/a
15	chr19:51400321-51400371	HCF	heart:	n/a
16	chr19:51400321-51400371	NHBE	bronchial:	n/a
17	chr19:51400352-51400402	PFSK-1	brain:	n/a
18	chr19:51400352-51400402	HL-60	blood:	n/a
19	chr19:51400352-51400402	A549	lung:	n/a
20	chr19:51400321-51400371	A549	lung:	n/a
21	chr19:51400321-51400371	HRCEpiC	kidney:	n/a
22	chr19:51400321-51400371	Jurkat	blood:	n/a
23	chr19:51400352-51400402	ovcar-3	ovarian:	n/a
24	chr19:51400321-51400371	PFSK-1	brain:	n/a
25	chr19:51400321-51400371	SAEC	small airway:	n/a
26	chr19:51400352-51400402	GM12892	blood:	n/a
27	chr19:51400352-51400402	HepG2	liver:	n/a
28	chr19:51400352-51400402	NHDF-neo	bronchial:	n/a
29	chr19:51400321-51400371	HEK293	kidney:	embryo
30	chr19:51400321-51400371	K562	blood:	n/a
31	chr19:51400352-51400402	MCF10A-Er-Src	breast:	n/a
32	chr19:51400352-51400402	LNCaP	prostate:	n/a
33	chr19:51400321-51400371	HPAEpiC	pulmonary alveolar:	n/a
34	chr19:51400352-51400402	HPAEpiC	pulmonary alveolar:	n/a
35	chr19:51400321-51400371	IMR90	lung:	fetal
36	chr19:51400321-51400371	HRPEpiC	eye:	n/a
37	chr19:51400352-51400402	PrEC	prostate:	n/a
38	chr19:51400352-51400402	Hela-S3	cervix:	n/a
39	chr19:51400321-51400371	SK-N-SH_RA	brain:	n/a
40	chr19:51400352-51400402	ECC-1	luminal epithelium:	n/a
41	chr19:51400321-51400371	NH-A	brain:	n/a
42	chr19:51400352-51400402	HCM	heart:	n/a
43	chr19:51400352-51400402	NH-A	brain:	n/a
44	chr19:51400352-51400402	HCF	heart:	n/a
45	chr19:51400352-51400402	RPTEC	kidney:	n/a
46	chr19:51400352-51400402	HEK293	kidney:	embryo
47	chr19:51400321-51400371	LNCaP	prostate:	n/a
48	chr19:51400321-51400371	AG09319	gingival:	n/a
49	chr19:51400352-51400402	PANC-1	pancreas:	n/a
50	chr19:51400321-51400371	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51305899..51307746-chr19:51399929..51401731,2	K562	blood:
2	chr19:51398902..51402347-chr19:51410482..51413710,3	K562	blood:
3	chr19:51398615..51401717-chr19:51409067..51411982,3	K562	blood:
4	chr19:51306246..51308382-chr19:51400037..51401731,2	K562	blood:
5	chr19:51297092..51299196-chr19:51400128..51402648,2	K562	blood:

Variant related genes	Relation type
KLKP1	TF binding region
KLKP1	CpG island
ENSG00000167749	Chromatin interaction
ENSG00000167747	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1654514	0.82[YRI][hapmap];0.91[AMR][1000 genomes]
rs1701934	0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2739481	1.00[GIH][hapmap]

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	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51397600-51400600	Enhancers	K562	blood
2	chr19:51399400-51401400	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:51399800-51400400	Enhancers	HSMMtube	muscle
4	chr19:51399800-51401000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:51399800-51401400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:51399800-51401600	Enhancers	HMEC	breast
7	chr19:51399800-51403000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:51400000-51400800	Enhancers	NHEK	skin
9	chr19:51400200-51401000	Flanking Active TSS	GM12878-XiMat	blood

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