Variant report

Variant	rs2659059
Chromosome Location	chr19:51308412-51308413
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	ZMIZ1	chr19:51307607-51308579	K562	blood:	n/a	n/a
2	POLR2A	chr19:51305171-51308575	Hela-S3	cervix:	n/a	n/a
3	MAX	chr19:51307397-51308657	SK-N-SH	brain:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
4	NR2F2	chr19:51307531-51308897	K562	blood:	n/a	n/a
5	MYC	chr19:51307575-51308547	MCF10A-Er-Src	breast:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
6	ELK1	chr19:51307652-51308538	K562	blood:	n/a	n/a
7	TCF12	chr19:51307651-51308431	ECC-1	luminal epithelium:	n/a	n/a
8	NFIC	chr19:51307479-51308454	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:51308078-51308565	GM12878	blood:	n/a	n/a
10	SP1	chr19:51307666-51308578	H1-hESC	embryonic stem cell:	n/a	chr19:51308226-51308235 chr19:51308055-51308062 chr19:51308224-51308236 chr19:51308277-51308291 chr19:51308280-51308292 chr19:51308282-51308291 chr19:51308280-51308292 chr19:51308224-51308236 chr19:51308281-51308290
11	WRNIP1	chr19:51307547-51308490	GM12878	blood:	n/a	n/a
12	USF1	chr19:51308075-51308547	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:51306817-51308499	MCF-7	breast:	n/a	n/a
14	ARID3A	chr19:51307814-51308412	HepG2	liver:	n/a	n/a
15	CHD2	chr19:51307501-51308595	Hela-S3	cervix:	n/a	chr19:51307601-51307611
16	MAX	chr19:51307546-51308491	H1-hESC	embryonic stem cell:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
17	RFX5	chr19:51307649-51308588	Hela-S3	cervix:	n/a	n/a
18	MYC	chr19:51307571-51308460	HUVEC	blood vessel:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
19	MAX	chr19:51306885-51308746	HCT-116	colon:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51307163-51307172 chr19:51308329-51308340
20	SIN3AK20	chr19:51307480-51308417	A549	lung:	n/a	n/a
21	ETS1	chr19:51307517-51308461	K562	blood:	n/a	chr19:51307795-51307804 chr19:51308375-51308384
22	SP1	chr19:51307688-51308471	K562	blood:	n/a	chr19:51308226-51308235 chr19:51308055-51308062 chr19:51308224-51308236 chr19:51308277-51308291 chr19:51308280-51308292 chr19:51308282-51308291 chr19:51308280-51308292 chr19:51308224-51308236 chr19:51308281-51308290
23	POLR2A	chr19:51307239-51308586	SK-N-MC	brain:	n/a	n/a
24	TAF1	chr19:51307329-51308544	K562	blood:	n/a	n/a
25	CEBPB	chr19:51307736-51308617	ECC-1	luminal epithelium:	n/a	chr19:51307784-51307796
26	GABPA	chr19:51308017-51308563	K562	blood:	n/a	n/a
27	CREB1	chr19:51307494-51308675	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:51306345-51308647	HL-60	blood:	n/a	n/a
29	FOXM1	chr19:51307493-51308511	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:51305218-51308754	SK-N-MC	brain:	n/a	n/a
31	REST	chr19:51307232-51308752	H1-neurons	neurons:	n/a	chr19:51308032-51308039 chr19:51308032-51308052 chr19:51307571-51307584 chr19:51308032-51308052
32	CEBPB	chr19:51308234-51308443	HepG2	liver:	n/a	n/a
33	MAX	chr19:51306993-51308542	K562	blood:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51307163-51307172 chr19:51308329-51308340
34	TAF1	chr19:51307205-51308602	H1-hESC	embryonic stem cell:	n/a	n/a
35	POU2F2	chr19:51307489-51308489	GM12891	blood:	n/a	chr19:51308278-51308290 chr19:51308220-51308232
36	ATF2	chr19:51307529-51308448	GM12878	blood:	n/a	n/a
37	HDAC2	chr19:51307540-51308671	MCF-7	breast:	n/a	n/a
38	CEBPB	chr19:51307677-51308567	IMR90	lung:	n/a	chr19:51307784-51307796
39	MAFK	chr19:51307675-51308574	Hela-S3	cervix:	n/a	n/a
40	MXI1	chr19:51306560-51308750	IMR90	lung:	n/a	chr19:51308329-51308338 chr19:51308331-51308340
41	ZBTB7A	chr19:51308187-51308632	ECC-1	luminal epithelium:	n/a	n/a
42	USF1	chr19:51308005-51308562	A549	lung:	n/a	n/a
43	YY1	chr19:51307000-51308447	GM12878	blood:	n/a	chr19:51307516-51307524 chr19:51307503-51307525 chr19:51307514-51307522 chr19:51307731-51307750 chr19:51307508-51307527 chr19:51307515-51307525 chr19:51308278-51308292
44	ELK1	chr19:51307645-51308589	GM12878	blood:	n/a	n/a
45	MAX	chr19:51307498-51308567	SK-N-SH	brain:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
46	TBP	chr19:51307033-51308460	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF1	chr19:51307191-51308582	ECC-1	luminal epithelium:	n/a	n/a
48	MYC	chr19:51306974-51308659	A549	lung:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51307163-51307172 chr19:51308329-51308340
49	SIN3AK20	chr19:51306850-51308702	MCF-7	breast:	n/a	n/a
50	POLR2A	chr19:51308167-51308585	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:51308364-51308414	IMR90	lung:	fetal
2	chr19:51308370-51308420	GM12891	blood:	n/a
3	chr19:51308364-51308414	HNPCEpiC	eye:	n/a
4	chr19:51308370-51308420	HCF	heart:	n/a
5	chr19:51308364-51308414	Hela-S3	cervix:	n/a
6	chr19:51308364-51308414	HPAEpiC	pulmonary alveolar:	n/a
7	chr19:51308364-51308414	AG10803	skin:	n/a
8	chr19:51308370-51308420	HepG2	liver:	n/a
9	chr19:51308370-51308420	Jurkat	blood:	n/a
10	chr19:51308364-51308414	GM12891	blood:	n/a
11	chr19:51308364-51308414	U87	brain:	n/a
12	chr19:51308370-51308420	HIPEpiC	eye:	n/a
13	chr19:51308364-51308414	CMK	blood:	n/a
14	chr19:51308364-51308414	NB4	blood:	n/a
15	chr19:51308370-51308420	NHBE	bronchial:	n/a
16	chr19:51308370-51308420	AG04450	lung:	fetal
17	chr19:51308370-51308420	U87	brain:	n/a
18	chr19:51308370-51308420	Hela-S3	cervix:	n/a
19	chr19:51308370-51308420	ECC-1	luminal epithelium:	n/a
20	chr19:51308370-51308420	HCM	heart:	n/a
21	chr19:51308370-51308420	LNCaP	prostate:	n/a
22	chr19:51308370-51308420	Caco-2	colon:	n/a
23	chr19:51308364-51308414	HRPEpiC	eye:	n/a
24	chr19:51308370-51308420	GM12878	blood:	n/a
25	chr19:51308364-51308414	PFSK-1	brain:	n/a
26	chr19:51308370-51308420	AG10803	skin:	n/a
27	chr19:51308364-51308414	LNCaP	prostate:	n/a
28	chr19:51308364-51308414	HCPEpiC	choroid plexus:	n/a
29	chr19:51308364-51308414	BJ	skin:	n/a
30	chr19:51308370-51308420	NT2-D1	testis:	n/a
31	chr19:51308364-51308414	RPTEC	kidney:	n/a
32	chr19:51308370-51308420	NH-A	brain:	n/a
33	chr19:51308370-51308420	AG04449	skin:	fetal
34	chr19:51308370-51308420	SK-N-MC	brain:	n/a
35	chr19:51308364-51308414	HRE	kidney:	n/a
36	chr19:51308370-51308420	T-47D	breast:	n/a
37	chr19:51308364-51308414	HAEpiC	amniotic membrane:	n/a
38	chr19:51308370-51308420	ProgFib	skin:	n/a
39	chr19:51308364-51308414	MCF-7	breast:	n/a
40	chr19:51308364-51308414	PANC-1	pancreas:	n/a
41	chr19:51308370-51308420	SAEC	small airway:	n/a
42	chr19:51308370-51308420	HAEpiC	amniotic membrane:	n/a
43	chr19:51308364-51308414	A549	lung:	n/a
44	chr19:51308370-51308420	ovcar-3	ovarian:	n/a
45	chr19:51308364-51308414	NH-A	brain:	n/a
46	chr19:51308370-51308420	SK-N-SH_RA	brain:	n/a
47	chr19:51308364-51308414	Caco-2	colon:	n/a
48	chr19:51308370-51308420	AG09309	skin:	n/a
49	chr19:51308370-51308420	IMR90	lung:	fetal
50	chr19:51308370-51308420	Hepatocyte	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51225685..51229614-chr19:51306371..51310193,7	MCF-7	breast:
2	chr19:51308172..51309760-chr19:51328581..51330697,2	MCF-7	breast:
3	chr19:51306849..51308707-chr19:51324714..51327546,2	MCF-7	breast:
4	chr19:50878289..50880426-chr19:51306206..51308776,2	K562	blood:
5	chr19:51225811..51229710-chr19:51304326..51309315,7	K562	blood:
6	chr19:51306828..51309257-chr19:51411309..51414080,2	MCF-7	breast:
7	chr19:51306795..51309015-chr19:51522024..51524887,2	K562	blood:
8	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
9	chr12:96793648..96794758-chr19:51307794..51308653,3	Hela-S3	cervix:
10	chr19:51306448..51310717-chr19:51372415..51375235,4	K562	blood:
11	chr19:51306173..51309320-chr19:51331029..51336004,5	MCF-7	breast:
12	chr19:51306202..51308468-chr19:51372838..51375377,2	K562	blood:
13	chr19:50878669..50883054-chr19:51306301..51308717,4	MCF-7	breast:
14	chr1:173836321..173837254-chr19:51307613..51308582,2	Hela-S3	cervix:
15	chr19:51305954..51309003-chr19:51339405..51341608,4	K562	blood:

Variant related genes	Relation type
C19orf48	TF binding region
SNORD88C	TF binding region
SNORD88C	CpG island
C19orf48	CpG island
ENSG00000131408	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000167749	Chromatin interaction
ENSG00000180279	Chromatin interaction
ENSG00000167748	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000129451	Chromatin interaction
ENSG00000267968	Chromatin interaction
ENSG00000174562	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000105472	Chromatin interaction
ENSG00000059758	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10425724	0.85[ASN][1000 genomes]
rs1054713	0.86[ASN][1000 genomes]
rs11672844	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197589	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1978605	0.95[ASN][1000 genomes]
rs2247289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411334	0.90[ASN][1000 genomes]
rs2434449	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456584	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2456585	0.97[ASN][1000 genomes]
rs2560931	0.97[ASN][1000 genomes]
rs2560933	0.97[ASN][1000 genomes]
rs2659058	0.83[ASN][1000 genomes]
rs2659061	0.90[AFR][1000 genomes]
rs2659099	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2659100	0.90[ASN][1000 genomes]
rs2659101	0.88[ASN][1000 genomes]
rs2659103	0.84[ASN][1000 genomes]
rs2659104	0.84[ASN][1000 genomes]
rs266116	0.91[ASN][1000 genomes]
rs266122	0.97[ASN][1000 genomes]
rs266123	0.97[ASN][1000 genomes]
rs266125	0.97[ASN][1000 genomes]
rs266127	0.97[ASN][1000 genomes]
rs266128	0.92[ASN][1000 genomes]
rs5516	0.88[ASN][1000 genomes]
rs56164547	0.82[ASN][1000 genomes]
rs59524380	0.82[ASN][1000 genomes]
rs788886	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs788887	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs788889	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788890	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788891	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv519121	chr19:51308092-51332670	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2659059	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51305800-51309000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:51306000-51308600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:51306000-51308600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:51306000-51309000	Active TSS	Colonic Mucosa	Colon
5	chr19:51306200-51308600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:51306200-51308600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:51306200-51308600	Active TSS	Fetal Intestine Large	intestine
8	chr19:51306200-51308800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:51306200-51308800	Active TSS	NHLF	lung
10	chr19:51306400-51308600	Active TSS	Esophagus	oesophagus
11	chr19:51306400-51308800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr19:51306400-51308800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:51306400-51308800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:51306400-51308800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:51306400-51308800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:51306400-51308800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:51306400-51309000	Active TSS	GM12878-XiMat	blood
18	chr19:51306600-51308600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:51306600-51308600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:51306600-51308600	Active TSS	Fetal Intestine Small	intestine
21	chr19:51306600-51308800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:51306600-51308800	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr19:51306600-51308800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:51306600-51308800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:51306600-51308800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:51306600-51308800	Active TSS	Fetal Kidney	kidney
27	chr19:51306600-51308800	Active TSS	NH-A	brain
28	chr19:51306600-51308800	Active TSS	NHDF-Ad	bronchial
29	chr19:51306800-51308600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr19:51306800-51308600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:51306800-51308600	Active TSS	Ovary	ovary
32	chr19:51306800-51308800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:51307000-51308600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr19:51307000-51308600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:51307000-51308600	Active TSS	Hela-S3	cervix
36	chr19:51307000-51308800	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr19:51307000-51308800	Active TSS	Fetal Lung	lung
38	chr19:51307000-51309000	Active TSS	K562	blood
39	chr19:51307200-51308600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr19:51307200-51308600	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr19:51307200-51308600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr19:51307200-51308600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:51307200-51308600	Active TSS	Aorta	Aorta
44	chr19:51307200-51308600	Active TSS	Gastric	stomach
45	chr19:51307200-51308600	Active TSS	Lung	lung
46	chr19:51307200-51308600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr19:51307200-51308600	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:51307200-51308600	Active TSS	Rectal Smooth Muscle	rectum
49	chr19:51307200-51308600	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr19:51307200-51308600	Active TSS	Small Intestine	intestine

The 2.0 version of rSNPBase

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