Variant report

Variant	rs2456585
Chromosome Location	chr19:51304104-51304105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51296363-51305119	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:51303995-51304945	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:51303946-51304824	K562	blood:	n/a	n/a
4	ZNF384	chr19:51303937-51304127	K562	blood:	n/a	n/a
5	POLR2A	chr19:51303960-51304794	GM12891	blood:	n/a	n/a
6	HEY1	chr19:51303981-51304841	K562	blood:	n/a	n/a
7	POLR2A	chr19:51296918-51304711	K562	blood:	n/a	n/a
8	POLR2A	chr19:51303874-51304329	K562	blood:	n/a	n/a
9	POLR2A	chr19:51303981-51304958	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:51292766-51304914	Hela-S3	cervix:	n/a	n/a
11	ZNF384	chr19:51303951-51304413	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:51303987-51304839	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr19:51304055-51304842	K562	blood:	n/a	n/a
14	POLR2A	chr19:51304028-51304738	K562	blood:	n/a	n/a
15	POLR2A	chr19:51304065-51304680	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:51304030-51304722	K562	blood:	n/a	n/a
17	POLR2A	chr19:51304020-51304752	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:51304008-51304719	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:51304032-51304419	HCT-116	colon:	n/a	n/a
20	POLR2A	chr19:51303983-51304678	MCF10A-Er-Src	breast:	n/a	n/a
21	USF2	chr19:51304049-51304537	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:51304036-51304250	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:51304039-51304778	HL-60	blood:	n/a	n/a
24	POLR2A	chr19:51303972-51304879	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:51291972-51304763	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr19:51304028-51304790	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:51296736-51304969	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr19:51303946-51304751	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr19:51303943-51304710	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr19:51297052-51304652	K562	blood:	n/a	n/a
31	POLR2A	chr19:51303948-51304773	GM12891	blood:	n/a	n/a
32	POLR2A	chr19:51303975-51304838	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr19:51295334-51304781	K562	blood:	n/a	n/a
34	POLR2A	chr19:51304019-51304855	GM12891	blood:	n/a	n/a
35	POLR2A	chr19:51304051-51304266	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:51304023-51304597	GM12891	blood:	n/a	n/a
37	POLR2A	chr19:51303878-51304947	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:51294975-51304879	GM12892	blood:	n/a	n/a
39	POLR2A	chr19:51294617-51304840	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr19:51295646-51304858	PFSK-1	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51303704..51306185-chr19:51373080..51375734,4	K562	blood:
2	chr19:51303704..51305752-chr19:51372094..51375734,4	K562	blood:
3	chr19:51103969..51106972-chr19:51302826..51304990,3	K562	blood:
4	chr19:51302089..51304601-chr19:51610266..51612462,2	K562	blood:
5	chr19:51291326..51293896-chr19:51301181..51304163,3	MCF-7	breast:

No data

Variant related genes	Relation type
SNORD88A	TF binding region
SNORD88B	TF binding region
ENSG00000167751	Chromatin interaction
ENSG00000142544	Chromatin interaction
ENSG00000142513	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10425724	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1054713	0.85[ASN][1000 genomes]
rs11672844	0.97[ASN][1000 genomes]
rs197589	0.90[ASN][1000 genomes]
rs1978605	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247289	0.97[ASN][1000 genomes]
rs2411334	0.89[ASN][1000 genomes]
rs2434449	0.97[ASN][1000 genomes]
rs2456584	0.97[ASN][1000 genomes]
rs2560931	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659058	0.82[ASN][1000 genomes]
rs2659059	0.97[ASN][1000 genomes]
rs2659099	0.90[ASN][1000 genomes]
rs2659100	0.89[ASN][1000 genomes]
rs2659101	0.86[ASN][1000 genomes]
rs2659103	0.83[ASN][1000 genomes]
rs2659104	0.83[ASN][1000 genomes]
rs266116	0.90[ASN][1000 genomes]
rs266122	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266123	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266125	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266127	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266128	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5516	0.86[ASN][1000 genomes]
rs56164547	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59524380	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs788886	0.93[ASN][1000 genomes]
rs788887	0.94[ASN][1000 genomes]
rs788889	0.97[ASN][1000 genomes]
rs788890	0.97[ASN][1000 genomes]
rs788891	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2456585	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51296600-51304200	Weak transcription	HSMM	muscle
2	chr19:51297000-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:51297600-51304200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:51297800-51305600	Weak transcription	Fetal Brain Male	brain
5	chr19:51297800-51306200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:51298000-51305400	Weak transcription	Fetal Heart	heart
7	chr19:51298200-51305400	Strong transcription	Fetal Intestine Small	intestine
8	chr19:51298200-51305400	Strong transcription	Fetal Stomach	stomach
9	chr19:51298200-51305800	Strong transcription	Brain Germinal Matrix	brain
10	chr19:51298200-51306000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:51298200-51306800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr19:51298400-51304400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:51298400-51304600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:51298400-51305400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:51298400-51305400	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:51298400-51305800	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:51298600-51304600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr19:51298600-51305000	Strong transcription	Thymus	Thymus
19	chr19:51298600-51305200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr19:51298600-51305400	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr19:51298600-51305400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:51298600-51305400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:51298600-51305400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:51298600-51305600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:51298600-51305600	Strong transcription	Fetal Brain Female	brain
26	chr19:51298800-51304600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:51298800-51305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:51298800-51305400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:51298800-51305400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:51298800-51305400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:51298800-51305600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:51299000-51304200	Strong transcription	HMEC	breast
33	chr19:51299000-51305400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:51299000-51305400	Strong transcription	Liver	Liver
35	chr19:51299200-51305800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:51299400-51305000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:51299400-51305400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:51299400-51305600	Weak transcription	NHDF-Ad	bronchial
39	chr19:51299400-51305800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:51299600-51304600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:51299600-51305400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr19:51299600-51305400	Strong transcription	NHEK	skin
43	chr19:51299600-51305800	Strong transcription	Lung	lung
44	chr19:51299800-51305000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr19:51299800-51305000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:51299800-51305600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:51299800-51305600	Strong transcription	Placenta	Placenta
48	chr19:51300000-51304800	Strong transcription	Right Ventricle	heart
49	chr19:51300000-51305000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:51300000-51305000	Strong transcription	Adipose Nuclei	Adipose

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