Variant report

Variant	rs2659099
Chromosome Location	chr19:51320607-51320608
allele	G/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	BCLAF1	chr19:51320535-51321316	GM12878	blood:	n/a	chr19:51320803-51320812
2	WRNIP1	chr19:51320389-51321109	GM12878	blood:	n/a	n/a
3	IRF4	chr19:51320580-51321275	GM12878	blood:	n/a	n/a
4	MTA3	chr19:51320351-51321220	GM12878	blood:	n/a	n/a
5	RELA	chr19:51320487-51321171	GM19099	blood:	n/a	n/a
6	ATF2	chr19:51320578-51321230	GM12878	blood:	n/a	n/a
7	YY1	chr19:51320443-51321004	GM12891	blood:	n/a	chr19:51320802-51320811
8	BCLAF1	chr19:51320496-51321301	GM12878	blood:	n/a	chr19:51320803-51320812
9	YY1	chr19:51320599-51321087	K562	blood:	n/a	chr19:51320802-51320811
10	ELF1	chr19:51320554-51321223	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:51320487-51323708	GM19193	blood:	n/a	n/a
12	RUNX3	chr19:51320387-51322054	GM12878	blood:	n/a	n/a
13	PML	chr19:51320312-51321896	GM12878	blood:	n/a	n/a
14	NFATC1	chr19:51320535-51321236	GM12878	blood:	n/a	n/a
15	CHD2	chr19:51320557-51321940	GM12878	blood:	n/a	chr19:51320696-51320706
16	YY1	chr19:51320467-51320974	GM12891	blood:	n/a	chr19:51320802-51320811
17	POU2F2	chr19:51320493-51321211	GM12891	blood:	n/a	n/a
18	FOXM1	chr19:51320509-51321373	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:51320412-51321995	GM12891	blood:	n/a	n/a
20	RELA	chr19:51320501-51321896	GM18951	blood:	n/a	n/a
21	STAT1	chr19:51320589-51321953	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:51320485-51324511	GM18526	blood:	n/a	n/a
23	POLR2A	chr19:51320314-51322404	GM12891	blood:	n/a	n/a
24	TBL1XR1	chr19:51320485-51321958	GM12878	blood:	n/a	n/a
25	USF2	chr19:51320404-51321897	GM12878	blood:	n/a	n/a
26	ATF2	chr19:51320470-51321332	GM12878	blood:	n/a	n/a
27	YY1	chr19:51320274-51321216	GM12878	blood:	n/a	chr19:51320802-51320811
28	NFIC	chr19:51320487-51321845	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:51320404-51324500	GM18951	blood:	n/a	n/a
30	EBF1	chr19:51320606-51321229	GM12878	blood:	n/a	chr19:51320902-51320911 chr19:51320901-51320912 chr19:51320902-51320912
31	EP300	chr19:51320433-51321195	GM12878	blood:	n/a	n/a
32	BCL3	chr19:51320575-51321193	GM12878	blood:	n/a	chr19:51320803-51320812
33	POLR2A	chr19:51320266-51322409	K562	blood:	n/a	n/a
34	POLR2A	chr19:51320353-51321985	GM12892	blood:	n/a	n/a
35	POLR2A	chr19:51320432-51321200	GM12892	blood:	n/a	n/a
36	PAX5	chr19:51320602-51321337	GM12878	blood:	n/a	n/a
37	NFYB	chr19:51320555-51320905	GM12878	blood:	n/a	n/a
38	EBF1	chr19:51320445-51322011	GM12878	blood:	n/a	chr19:51320902-51320911 chr19:51320901-51320912 chr19:51320902-51320912
39	POLR2A	chr19:51320487-51322076	GM19099	blood:	n/a	n/a
40	YY1	chr19:51320419-51321073	GM12892	blood:	n/a	chr19:51320802-51320811
41	STAT3	chr19:51320484-51321099	GM12878	blood:	n/a	n/a
42	MEF2C	chr19:51320606-51321235	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:51320473-51321264	GM12878	blood:	n/a	n/a
44	YY1	chr19:51320377-51321201	GM12892	blood:	n/a	chr19:51320802-51320811
45	MTA3	chr19:51320135-51321868	GM12878	blood:	n/a	n/a
46	MAX	chr19:51320518-51322010	GM12878	blood:	n/a	n/a
47	NFATC1	chr19:51320499-51321350	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:51320230-51323607	GM12878	blood:	n/a	n/a
49	STAT5A	chr19:51320593-51321343	GM12878	blood:	n/a	n/a
50	MAZ	chr19:51320282-51322562	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51319200..51320896-chr19:51322440..51324898,2	MCF-7	breast:
2	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
3	chr19:51317914..51322870-chr19:51325257..51328084,4	MCF-7	breast:
4	chr19:51305829..51307927-chr19:51320436..51323745,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180279	TF binding region
ENSG00000167747	Chromatin interaction
ENSG00000167748	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10425724	0.81[ASN][1000 genomes]
rs1054713	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11672844	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs197589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978605	0.89[ASN][1000 genomes]
rs2247289	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2411334	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2434449	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2456584	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456585	0.90[ASN][1000 genomes]
rs2560931	0.90[ASN][1000 genomes]
rs2560933	0.90[ASN][1000 genomes]
rs2659058	0.92[ASN][1000 genomes]
rs2659059	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2659100	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659101	0.96[ASN][1000 genomes]
rs2659103	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2659104	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs266116	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266122	0.90[ASN][1000 genomes]
rs266123	0.90[ASN][1000 genomes]
rs266125	0.90[ASN][1000 genomes]
rs266127	0.90[ASN][1000 genomes]
rs266128	0.86[ASN][1000 genomes]
rs5516	0.96[ASN][1000 genomes]
rs788886	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs788887	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs788889	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs788890	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs788891	0.82[AMR][1000 genomes];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2659099	C19orf48	Cis_1M	lymphoblastoid	RTeQTL
rs2659099	KLK1	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51320200-51321200	Enhancers	Primary B cells from peripheral blood	blood
2	chr19:51320400-51320800	Flanking Active TSS	GM12878-XiMat	blood
3	chr19:51320400-51321000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
4	chr19:51320400-51321000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:51320400-51321000	Enhancers	K562	blood
6	chr19:51320600-51320800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr19:51320600-51320800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:51320600-51320800	Bivalent Enhancer	Brain Anterior Caudate	brain
9	chr19:51320600-51320800	Flanking Active TSS	HMEC	breast
10	chr19:51320600-51320800	Enhancers	NHEK	skin
11	chr19:51320600-51321000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:51320600-51321000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr19:51320600-51321000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:51320600-51321400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr19:51320600-51321400	Enhancers	Pancreas	Pancrea
16	chr19:51320600-51322000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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