Variant report

Variant	rs12983994
Chromosome Location	chr19:51373744-51373745
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	CREB1	chr19:51373611-51374186	GM12878	blood:	n/a	chr19:51373839-51373852
2	CTCF	chr19:51373740-51373890	RPTEC	kidney:	n/a	n/a
3	CREB1	chr19:51373521-51374108	HepG2	liver:	n/a	chr19:51373839-51373852
4	EBF1	chr19:51373713-51374005	GM12878	blood:	n/a	n/a
5	ATF3	chr19:51373692-51374085	GM12878	blood:	n/a	chr19:51373842-51373849 chr19:51373842-51373852 chr19:51373838-51373853 chr19:51373830-51373850 chr19:51373841-51373861 chr19:51373841-51373849 chr19:51373839-51373849 chr19:51373842-51373850 chr19:51373838-51373851 chr19:51373839-51373852 chr19:51373839-51373849
6	POLR2A	chr19:51373652-51374105	K562	blood:	n/a	n/a
7	TBL1XR1	chr19:51373670-51374069	K562	blood:	n/a	n/a
8	CTCF	chr19:51373524-51374240	SK-N-SH	brain:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373728-51373744 chr19:51373916-51373926 chr19:51373908-51373929
9	YY1	chr19:51373675-51374038	A549	lung:	n/a	n/a
10	HEY1	chr19:51373610-51373973	K562	blood:	n/a	chr19:51373840-51373849 chr19:51373824-51373839 chr19:51373842-51373851
11	SP1	chr19:51373621-51374143	A549	lung:	n/a	n/a
12	HCFC1	chr19:51373634-51374103	K562	blood:	n/a	n/a
13	CREB1	chr19:51373636-51374085	ECC-1	luminal epithelium:	n/a	chr19:51373839-51373852
14	POLR2A	chr19:51373695-51373916	A549	lung:	n/a	n/a
15	NR2F2	chr19:51373687-51374170	K562	blood:	n/a	n/a
16	MYC	chr19:51373610-51374111	K562	blood:	n/a	n/a
17	MYC	chr19:51373624-51374117	K562	blood:	n/a	n/a
18	RAD21	chr19:51373738-51374126	A549	lung:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
19	MAFF	chr19:51373723-51373883	K562	blood:	n/a	n/a
20	ATF3	chr19:51373673-51374060	K562	blood:	n/a	chr19:51373842-51373849 chr19:51373842-51373852 chr19:51373838-51373853 chr19:51373830-51373850 chr19:51373841-51373861 chr19:51373841-51373849 chr19:51373839-51373849 chr19:51373842-51373850 chr19:51373838-51373851 chr19:51373839-51373852 chr19:51373839-51373849
21	CTCF	chr19:51373550-51374369	A549	lung:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373728-51373744 chr19:51373916-51373926 chr19:51373908-51373929
22	ZNF384	chr19:51373721-51374032	K562	blood:	n/a	n/a
23	POLR2A	chr19:51373740-51373911	A549	lung:	n/a	n/a
24	SIX5	chr19:51373741-51374037	K562	blood:	n/a	n/a
25	EGR1	chr19:51373635-51374052	K562	blood:	n/a	chr19:51373740-51373749
26	MAX	chr19:51373581-51374035	K562	blood:	n/a	n/a
27	RAD21	chr19:51373714-51374024	K562	blood:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
28	TAF1	chr19:51373605-51373991	K562	blood:	n/a	n/a
29	ATF3	chr19:51373702-51374080	K562	blood:	n/a	chr19:51373842-51373849 chr19:51373842-51373852 chr19:51373838-51373853 chr19:51373830-51373850 chr19:51373841-51373861 chr19:51373841-51373849 chr19:51373839-51373849 chr19:51373842-51373850 chr19:51373838-51373851 chr19:51373839-51373852 chr19:51373839-51373849
30	RAD21	chr19:51373549-51374248	SK-N-SH	brain:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
31	BHLHE40	chr19:51373675-51374075	K562	blood:	n/a	n/a
32	CTCF	chr19:51373724-51373988	A549	lung:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373728-51373744 chr19:51373916-51373926 chr19:51373908-51373929
33	RAD21	chr19:51373729-51374099	K562	blood:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
34	MAX	chr19:51373467-51374205	A549	lung:	n/a	n/a
35	CREB1	chr19:51373646-51374066	A549	lung:	n/a	chr19:51373839-51373852
36	RUNX3	chr19:51373635-51374066	GM12878	blood:	n/a	n/a
37	YY1	chr19:51373697-51374121	K562	blood:	n/a	n/a
38	RCOR1	chr19:51373575-51374057	K562	blood:	n/a	n/a
39	MAX	chr19:51373641-51374084	K562	blood:	n/a	n/a
40	EP300	chr19:51373674-51374081	K562	blood:	n/a	n/a
41	SRF	chr19:51373636-51374021	K562	blood:	n/a	n/a
42	ZNF143	chr19:51373737-51374057	K562	blood:	n/a	n/a
43	CTCF	chr19:51373675-51374077	A549	lung:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373728-51373744 chr19:51373916-51373926 chr19:51373908-51373929
44	MAX	chr19:51373520-51374150	A549	lung:	n/a	n/a
45	CREB1	chr19:51373491-51374199	K562	blood:	n/a	chr19:51373839-51373852
46	SRF	chr19:51373699-51373968	GM12878	blood:	n/a	n/a
47	YY1	chr19:51373713-51374056	K562	blood:	n/a	n/a
48	MXI1	chr19:51373673-51373963	K562	blood:	n/a	n/a
49	SMC3	chr19:51373660-51374172	SK-N-SH	brain:	n/a	chr19:51373915-51373929 chr19:51373915-51373925
50	CREB1	chr19:51373534-51374164	GM12878	blood:	n/a	chr19:51373839-51373852

No.	Distal block	Cell Line	Cell type
1	chr19:51303704..51306185-chr19:51373080..51375734,4	K562	blood:
2	chr19:51339489..51342221-chr19:51372439..51375548,3	K562	blood:
3	chr19:51306448..51310717-chr19:51372415..51375235,4	K562	blood:
4	chr19:51304876..51308314-chr19:51372660..51375800,4	MCF-7	breast:
5	chr19:51372696..51375845-chr19:51379331..51383690,4	K562	blood:
6	chr19:51303704..51305752-chr19:51372094..51375734,4	K562	blood:
7	chr19:51292849..51296626-chr19:51372637..51375537,3	K562	blood:
8	chr19:51297152..51303261-chr19:51371696..51377038,8	K562	blood:
9	chr19:51306202..51308468-chr19:51372838..51375377,2	K562	blood:
10	chr19:51296429..51299323-chr19:51371370..51374659,5	K562	blood:

Variant related genes	Relation type
KLK2	TF binding region
ENSG00000268375	Chromatin interaction
ENSG00000220988	Chromatin interaction
ENSG00000142513	Chromatin interaction
ENSG00000221381	Chromatin interaction
ENSG00000167747	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000221241	Chromatin interaction
ENSG00000174562	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12946	0.85[ASN][1000 genomes]
rs12974899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978483	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34314776	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34532440	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34750956	0.87[ASN][1000 genomes]
rs35192866	0.89[ASN][1000 genomes]
rs3760722	1.00[JPT][hapmap]
rs45588133	0.87[ASN][1000 genomes]
rs66592214	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv2531	chr19:51333628-51378597	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2763208	chr19:51361757-51377163	ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12983994	KLK4	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51373200-51374200	Bivalent/Poised TSS	A549	lung
2	chr19:51373400-51374200	Bivalent/Poised TSS	HepG2	liver
3	chr19:51373400-51374400	Flanking Active TSS	K562	blood
4	chr19:51373600-51374200	Enhancers	Placenta	Placenta

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