Variant report

Variant	rs2560931
Chromosome Location	chr19:51305784-51305785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51305506-51305892	A549	lung:	n/a	n/a
2	POLR2A	chr19:51305171-51308575	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:51305218-51308754	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr19:51305400-51305811	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:51305245-51305784	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:51305213-51308097	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:51305153-51308634	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:51305170-51308571	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:51305179-51309471	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:51305427-51305800	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:51305452-51308828	K562	blood:	n/a	n/a
12	POLR2A	chr19:51305421-51305875	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:51305174-51308584	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:51305338-51308648	GM12891	blood:	n/a	n/a
15	HEY1	chr19:51305231-51308447	K562	blood:	n/a	chr19:51307531-51307546
16	POLR2A	chr19:51305359-51305788	K562	blood:	n/a	n/a
17	POLR2A	chr19:51305307-51308547	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr19:51305432-51305832	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:51305440-51305837	A549	lung:	n/a	n/a
20	POLR2A	chr19:51305464-51308657	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr19:51305373-51307998	A549	lung:	n/a	n/a
22	POLR2A	chr19:51305232-51306290	K562	blood:	n/a	n/a
23	POLR2A	chr19:51305496-51308422	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr19:51305364-51308607	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:51305176-51308591	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:51305256-51305842	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr19:51305396-51308628	GM19099	blood:	n/a	n/a
28	POLR2A	chr19:51305263-51307426	GM12891	blood:	n/a	n/a
29	POLR2A	chr19:51305314-51306276	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:51305034-51308640	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:51305200-51308131	GM12891	blood:	n/a	n/a
32	POLR2A	chr19:51305309-51308551	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr19:51305261-51305836	GM12892	blood:	n/a	n/a
34	POLR2A	chr19:51305326-51308592	K562	blood:	n/a	n/a
35	POLR2A	chr19:51305343-51308586	K562	blood:	n/a	n/a
36	POLR2A	chr19:51305272-51308541	K562	blood:	n/a	n/a
37	POLR2A	chr19:51305353-51305826	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr19:51305761-51308074	GM12891	blood:	n/a	n/a
39	POLR2A	chr19:51305191-51305880	PFSK-1	brain:	n/a	n/a
40	HEY1	chr19:51305435-51306266	K562	blood:	n/a	n/a
41	POLR2A	chr19:51305299-51306327	HL-60	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:51303704..51306185-chr19:51373080..51375734,4	K562	blood:
2	chr19:51304876..51308314-chr19:51372660..51375800,4	MCF-7	breast:
3	chr19:51225811..51229710-chr19:51304326..51309315,7	K562	blood:
4	chr19:51221053..51222783-chr19:51305600..51307865,2	K562	blood:

No data

Variant related genes	Relation type
SNORD88A	TF binding region
C19orf48	TF binding region
SNORD88C	TF binding region
SNORD88B	TF binding region
ENSG00000161681	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000105472	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	0.93[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]
rs2456585	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560933	0.89[AFR][1000 genomes];0.95[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	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266123	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266125	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266127	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266128	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5516	0.86[ASN][1000 genomes]
rs56164547	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59524380	0.88[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
rs2560931	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	chr19:51297000-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:51297800-51306200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:51298200-51305800	Strong transcription	Brain Germinal Matrix	brain
4	chr19:51298200-51306000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:51298200-51306800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:51298400-51305800	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:51299200-51305800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:51299400-51305800	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr19:51299600-51305800	Strong transcription	Lung	lung
10	chr19:51300000-51305800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:51300000-51306800	Weak transcription	Right Atrium	heart
12	chr19:51300200-51305800	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:51300400-51305800	Strong transcription	Ovary	ovary
14	chr19:51300800-51306200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:51301000-51305800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:51301200-51305800	Strong transcription	Osteobl	bone
17	chr19:51301800-51306000	Weak transcription	Stomach Mucosa	stomach
18	chr19:51302000-51306200	Weak transcription	Primary B cells from cord blood	blood
19	chr19:51302000-51306200	Weak transcription	Psoas Muscle	Psoas
20	chr19:51302000-51307200	Weak transcription	Aorta	Aorta
21	chr19:51302200-51305800	Weak transcription	Brain Angular Gyrus	brain
22	chr19:51302200-51306600	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:51302200-51306600	Weak transcription	Small Intestine	intestine
24	chr19:51302400-51306200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:51302400-51306200	Weak transcription	Brain Substantia Nigra	brain
26	chr19:51302400-51306200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:51302800-51307000	Transcr. at gene 5' and 3'	Hela-S3	cervix
28	chr19:51303000-51305800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:51303000-51306000	Weak transcription	Brain Anterior Caudate	brain
30	chr19:51303000-51306200	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:51303200-51305800	Strong transcription	Primary T cells from cord blood	blood
32	chr19:51304000-51306000	Weak transcription	Esophagus	oesophagus
33	chr19:51304200-51306000	Genic enhancers	HMEC	breast
34	chr19:51304400-51305800	Strong transcription	Left Ventricle	heart
35	chr19:51304400-51306200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:51304600-51305800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr19:51304600-51306000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:51304800-51306000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:51304800-51306000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr19:51304800-51306000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:51304800-51306000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:51304800-51306000	Weak transcription	Colonic Mucosa	Colon
43	chr19:51304800-51306200	Weak transcription	Right Ventricle	heart
44	chr19:51305000-51305800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:51305000-51305800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:51305000-51306000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr19:51305000-51306000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:51305000-51306000	Weak transcription	Adipose Nuclei	Adipose
49	chr19:51305000-51306000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:51305000-51306000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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