Variant report

Variant	rs10419880
Chromosome Location	chr19:51897392-51897393
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	MTA3	chr19:51897045-51899150	GM12878	blood:	n/a	n/a
2	GABPA	chr19:51897343-51898041	K562	blood:	n/a	chr19:51897759-51897768 chr19:51897837-51897846 chr19:51897837-51897848 chr19:51897834-51897848
3	NFYB	chr19:51897382-51897969	Hela-S3	cervix:	n/a	chr19:51897652-51897667 chr19:51897709-51897723 chr19:51897712-51897724 chr19:51897708-51897723 chr19:51897655-51897665 chr19:51897654-51897669 chr19:51897652-51897667 chr19:51897711-51897721 chr19:51897710-51897723 chr19:51897708-51897723
4	TAF1	chr19:51897208-51898127	A549	lung:	n/a	n/a
5	BHLHE40	chr19:51897307-51898007	K562	blood:	n/a	n/a
6	GABPA	chr19:51897315-51897788	Hela-S3	cervix:	n/a	chr19:51897759-51897768
7	CTCF	chr19:51897286-51897396	MCF-7	breast:	n/a	n/a
8	CTCF	chr19:51897286-51897420	Medullo	brain:	n/a	n/a
9	ZBTB7A	chr19:51897356-51898066	K562	blood:	n/a	n/a
10	ELF1	chr19:51897207-51898093	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:51897369-51898062	Gliobla	brain:	n/a	n/a
12	FOXM1	chr19:51897346-51898056	ECC-1	luminal epithelium:	n/a	n/a
13	ARID3A	chr19:51897142-51897847	K562	blood:	n/a	n/a
14	SRF	chr19:51897353-51897583	H1-hESC	embryonic stem cell:	n/a	chr19:51897462-51897480
15	YY1	chr19:51897135-51897558	GM12892	blood:	n/a	n/a
16	TAF1	chr19:51897166-51898200	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr19:51897212-51898083	K562	blood:	n/a	n/a
18	MYBL2	chr19:51897264-51897971	HepG2	liver:	n/a	n/a
19	TAL1	chr19:51897116-51897458	K562	blood:	n/a	n/a
20	SP1	chr19:51897233-51897935	H1-hESC	embryonic stem cell:	n/a	chr19:51897667-51897679 chr19:51897667-51897679 chr19:51897701-51897722 chr19:51897517-51897531
21	FOXM1	chr19:51897380-51897921	ECC-1	luminal epithelium:	n/a	n/a
22	YY1	chr19:51897253-51897623	SK-N-SH_RA	brain:	n/a	n/a
23	POLR2A	chr19:51897300-51897626	HepG2	liver:	n/a	n/a
24	ELF1	chr19:51897131-51897924	A549	lung:	n/a	n/a
25	RCOR1	chr19:51897276-51897953	HepG2	liver:	n/a	n/a
26	MAX	chr19:51897288-51898070	H1-hESC	embryonic stem cell:	n/a	n/a
27	CEBPB	chr19:51897307-51897602	K562	blood:	n/a	n/a
28	NFIC	chr19:51897088-51898048	GM12878	blood:	n/a	chr19:51897220-51897236 chr19:51897219-51897236
29	NFYA	chr19:51897358-51898020	K562	blood:	n/a	chr19:51897652-51897667 chr19:51897709-51897723 chr19:51897712-51897724 chr19:51897708-51897723 chr19:51897655-51897665 chr19:51897652-51897667 chr19:51897711-51897721 chr19:51897710-51897723 chr19:51897708-51897723
30	SP1	chr19:51897056-51898295	HCT-116	colon:	n/a	chr19:51897667-51897679 chr19:51897667-51897679 chr19:51897701-51897722 chr19:51897517-51897531
31	USF2	chr19:51897319-51897662	HepG2	liver:	n/a	n/a
32	GABPA	chr19:51897368-51897906	GM12878	blood:	n/a	chr19:51897759-51897768 chr19:51897837-51897846 chr19:51897837-51897848 chr19:51897834-51897848
33	MXI1	chr19:51896896-51898500	SK-N-SH	brain:	n/a	n/a
34	ZBTB7A	chr19:51897315-51898256	K562	blood:	n/a	n/a
35	POLR2A	chr19:51897294-51897530	SK-N-SH	brain:	n/a	n/a
36	TAF7	chr19:51897118-51897582	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr19:51897247-51898050	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZNF143	chr19:51897384-51897987	K562	blood:	n/a	n/a
39	TBP	chr19:51897195-51898039	GM12878	blood:	n/a	n/a
40	SRF	chr19:51897201-51898048	MCF-7	breast:	n/a	chr19:51897462-51897480
41	CTCF	chr19:51897260-51897410	GM12873	blood:	n/a	n/a
42	CTCF	chr19:51897380-51897530	Caco-2	colon:	n/a	n/a
43	TBL1XR1	chr19:51897190-51898004	GM12878	blood:	n/a	n/a
44	CTCF	chr19:51897320-51897470	BJ	skin:	n/a	n/a
45	CTCF	chr19:51897268-51897561	Spleen_OC	spleen:	n/a	n/a
46	TBL1XR1	chr19:51897358-51898319	K562	blood:	n/a	n/a
47	POLR2A	chr19:51897363-51898260	MCF-7	breast:	n/a	n/a
48	POLR2A	chr19:51897232-51899094	GM18951	blood:	n/a	n/a
49	IRF3	chr19:51897293-51897815	Hela-S3	cervix:	n/a	chr19:51897520-51897534 chr19:51897665-51897679 chr19:51897712-51897721
50	POLR2A	chr19:51897072-51898436	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51852221..51854655-chr19:51896063..51897608,2	K562	blood:
2	chr19:51869234..51872471-chr19:51897367..51899516,3	MCF-7	breast:
3	chr19:51895053..51897765-chr19:52007493..52009642,2	K562	blood:
4	chr19:51897297..51899400-chr19:52095029..52099296,3	K562	blood:
5	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
6	chr19:51896400..51903695-chr19:51903717..51912186,11	K562	blood:
7	chr19:51894435..51896093-chr19:51896097..51897636,2	K562	blood:
8	chr19:51847346..51848930-chr19:51897301..51899895,2	K562	blood:
9	chr19:51841257..51845442-chr19:51896216..51899567,12	K562	blood:
10	chr19:51896384..51897937-chr19:51904154..51907057,2	MCF-7	breast:
11	chr19:51897392..51898223-chr9:20684270..20685038,2	Hela-S3	cervix:
12	chr19:51867772..51875803-chr19:51892381..51899756,21	K562	blood:
13	chr19:51864453..51872845-chr19:51892428..51902096,29	K562	blood:
14	chr19:51889349..51894566-chr19:51895156..51899826,6	K562	blood:
15	chr19:51868903..51871265-chr19:51897328..51899243,2	MCF-7	breast:
16	chr19:51889722..51893942-chr19:51894149..51900029,8	K562	blood:

Variant related genes	Relation type
ENSG00000268889	TF binding region
C19orf84	TF binding region
ENSG00000105379	Chromatin interaction
ENSG00000267984	Chromatin interaction
ENSG00000105370	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000267905	Chromatin interaction
ENSG00000268839	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000227071	Chromatin interaction
ENSG00000268144	Chromatin interaction
ENSG00000105374	Chromatin interaction
ENSG00000167765	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000262874	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000160318	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10403762	0.81[ASN][1000 genomes]
rs10404198	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11084075	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11084076	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11084077	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11669975	0.92[ASN][1000 genomes]
rs11670065	0.92[ASN][1000 genomes]
rs11673263	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17729239	0.89[CEU][hapmap];0.92[TSI][hapmap]
rs17802282	0.86[CEU][hapmap]
rs2411321	0.91[ASN][1000 genomes]
rs2411322	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2547308	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2547309	0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2741240	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2741241	0.83[ASN][1000 genomes]
rs3810093	0.92[ASN][1000 genomes]
rs3810094	0.94[ASN][1000 genomes]
rs3810095	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3810096	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3810097	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3826657	0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3826658	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3826659	0.92[ASN][1000 genomes]
rs3826660	0.92[ASN][1000 genomes]
rs3826662	0.81[ASN][1000 genomes]
rs3826663	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3826664	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3826665	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4377257	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4441376	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7250926	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7251238	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7251311	0.92[ASN][1000 genomes]
rs7251566	0.92[ASN][1000 genomes]
rs7257275	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7508570	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8100861	0.92[ASN][1000 genomes]
rs8104425	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8107533	0.95[ASN][1000 genomes]
rs8111906	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51896800-51898000	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr19:51896800-51898200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:51896800-51898600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:51897000-51897400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
5	chr19:51897000-51897400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:51897000-51897400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr19:51897000-51897400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:51897000-51897400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr19:51897000-51897400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr19:51897000-51897400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr19:51897000-51897400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr19:51897000-51897400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr19:51897000-51897400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:51897000-51897400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:51897000-51897400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr19:51897000-51897400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr19:51897000-51897400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:51897000-51897400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:51897000-51897400	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr19:51897000-51897400	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr19:51897000-51897400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr19:51897000-51897400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr19:51897000-51897400	Enhancers	Esophagus	oesophagus
24	chr19:51897000-51897400	Flanking Active TSS	Fetal Brain Female	brain
25	chr19:51897000-51897400	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr19:51897000-51897400	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr19:51897000-51897400	Flanking Active TSS	A549	lung
28	chr19:51897000-51897400	Flanking Active TSS	Dnd41	blood
29	chr19:51897000-51897400	Flanking Active TSS	Hela-S3	cervix
30	chr19:51897000-51897400	Flanking Active TSS	HepG2	liver
31	chr19:51897000-51897400	Flanking Active TSS	NHDF-Ad	bronchial
32	chr19:51897000-51897400	Flanking Active TSS	NHEK	skin
33	chr19:51897000-51897400	Flanking Active TSS	Osteobl	bone
34	chr19:51897000-51897600	Active TSS	Brain Cingulate Gyrus	brain
35	chr19:51897000-51897800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:51897000-51897800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:51897000-51897800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:51897000-51897800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:51897000-51897800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:51897000-51897800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:51897000-51897800	Active TSS	Brain Angular Gyrus	brain
42	chr19:51897000-51897800	Active TSS	Brain Germinal Matrix	brain
43	chr19:51897000-51897800	Active TSS	Brain Hippocampus Middle	brain
44	chr19:51897000-51897800	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr19:51897000-51897800	Active TSS	Colonic Mucosa	Colon
46	chr19:51897000-51897800	Enhancers	Lung	lung
47	chr19:51897000-51897800	Active TSS	Psoas Muscle	Psoas
48	chr19:51897000-51897800	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:51897000-51897800	Active TSS	NHLF	lung
50	chr19:51897000-51898000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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