Variant report

Variant	rs12974899
Chromosome Location	chr19:51373899-51373900
allele	A/C
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	chr19:51373860-51374010	A549	lung:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
2	CREB1	chr19:51373611-51374186	GM12878	blood:	n/a	chr19:51373839-51373852
3	REST	chr19:51373879-51374175	K562	blood:	n/a	chr19:51374026-51374035
4	CTCF	chr19:51373880-51374030	HPAF	blood vessel:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
5	CTCF	chr19:51373789-51374046	A549	lung:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
6	CTCF	chr19:51373860-51374010	GM12875	blood:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
7	CREB1	chr19:51373521-51374108	HepG2	liver:	n/a	chr19:51373839-51373852
8	EBF1	chr19:51373713-51374005	GM12878	blood:	n/a	n/a
9	UBTF	chr19:51373850-51374053	K562	blood:	n/a	n/a
10	CTCF	chr19:51373860-51374010	SK-N-SH_RA	brain:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
11	CTCF	chr19:51373828-51373994	GM19238	blood:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
12	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
13	POLR2A	chr19:51373652-51374105	K562	blood:	n/a	n/a
14	TBL1XR1	chr19:51373670-51374069	K562	blood:	n/a	n/a
15	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
16	YY1	chr19:51373675-51374038	A549	lung:	n/a	n/a
17	CTCF	chr19:51373794-51373999	HepG2	liver:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
18	HEY1	chr19:51373610-51373973	K562	blood:	n/a	chr19:51373840-51373849 chr19:51373824-51373839 chr19:51373842-51373851
19	SP1	chr19:51373621-51374143	A549	lung:	n/a	n/a
20	HCFC1	chr19:51373634-51374103	K562	blood:	n/a	n/a
21	CREB1	chr19:51373636-51374085	ECC-1	luminal epithelium:	n/a	chr19:51373839-51373852
22	POLR2A	chr19:51373695-51373916	A549	lung:	n/a	n/a
23	CTCF	chr19:51373880-51374030	WI-38	lung:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
24	NR2F2	chr19:51373687-51374170	K562	blood:	n/a	n/a
25	MYC	chr19:51373610-51374111	K562	blood:	n/a	n/a
26	CTCF	chr19:51373784-51373960	A549	lung:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
27	MYC	chr19:51373624-51374117	K562	blood:	n/a	n/a
28	RAD21	chr19:51373738-51374126	A549	lung:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
29	POLR2A	chr19:51373747-51373977	K562	blood:	n/a	n/a
30	CTCF	chr19:51373840-51373990	HCM	heart:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
31	SIX5	chr19:51373750-51374022	K562	blood:	n/a	n/a
32	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
33	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
34	CTCF	chr19:51373820-51373970	HMF	breast:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
35	ZNF384	chr19:51373721-51374032	K562	blood:	n/a	n/a
36	CTCF	chr19:51373880-51374030	GM12871	blood:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
37	RAD21	chr19:51373749-51374116	H1-hESC	embryonic stem cell:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
38	POLR2A	chr19:51373740-51373911	A549	lung:	n/a	n/a
39	CTCF	chr19:51373771-51374057	GM12891	blood:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
40	SIX5	chr19:51373741-51374037	K562	blood:	n/a	n/a
41	EGR1	chr19:51373635-51374052	K562	blood:	n/a	chr19:51373740-51373749
42	MAX	chr19:51373581-51374035	K562	blood:	n/a	n/a
43	CTCF	chr19:51373860-51374010	GM06990	blood:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
44	RAD21	chr19:51373714-51374024	K562	blood:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
45	TAF1	chr19:51373605-51373991	K562	blood:	n/a	n/a
46	CTCF	chr19:51373840-51373990	GM12873	blood:	n/a	chr19:51373919-51373928 chr19:51373914-51373930 chr19:51373913-51373931 chr19:51373916-51373926 chr19:51373908-51373929
47	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
48	RAD21	chr19:51373549-51374248	SK-N-SH	brain:	n/a	chr19:51373915-51373925 chr19:51373911-51373930
49	BHLHE40	chr19:51373675-51374075	K562	blood:	n/a	n/a
50	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

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	chr19:51373828..51375364-chr19:51376061..51378763,2	K562	blood:
7	chr19:51303704..51305752-chr19:51372094..51375734,4	K562	blood:
8	chr19:51292849..51296626-chr19:51372637..51375537,3	K562	blood:
9	chr19:51297152..51303261-chr19:51371696..51377038,8	K562	blood:
10	chr19:51306202..51308468-chr19:51372838..51375377,2	K562	blood:
11	chr19:51296429..51299323-chr19:51371370..51374659,5	K562	blood:

Variant related genes	Relation type
KLK2	TF binding region
ENSG00000174562	Chromatin interaction
ENSG00000221241	Chromatin interaction
ENSG00000221381	Chromatin interaction
ENSG00000142513	Chromatin interaction
ENSG00000267880	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000167747	Chromatin interaction
ENSG00000268375	Chromatin interaction
ENSG00000220988	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]
rs12978483	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12983994	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]
rs2003783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34314776	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34532440	0.81[AMR][1000 genomes];0.85[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
rs12974899	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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