Variant report

Variant	rs13345246
Chromosome Location	chr19:19101218-19101219
allele	A/G
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	POLR2A	chr19:19100873-19101306	Hela-S3	cervix:	n/a	n/a
2	HMGN3	chr19:19101050-19101252	K562	blood:	n/a	n/a
3	POLR2A	chr19:19100779-19101245	H1-neurons	neurons:	n/a	n/a
4	FOSL2	chr19:19100579-19101264	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:19100804-19101581	K562	blood:	n/a	n/a
6	POLR2A	chr19:19100000-19101400	U87	brain:	n/a	n/a
7	POLR2A	chr19:19101070-19101256	A549	lung:	n/a	n/a
8	BCL3	chr19:19100705-19101625	K562	blood:	n/a	chr19:19101367-19101375
9	POLR2A	chr19:19100231-19101401	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr19:19100448-19101703	HL-60	blood:	n/a	n/a
11	POLR2A	chr19:19100132-19101475	MCF-7	breast:	n/a	n/a
12	POLR2A	chr19:19100510-19101751	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr19:19100459-19101657	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:19100639-19101685	GM12892	blood:	n/a	n/a
15	BCL3	chr19:19100950-19101533	GM12878	blood:	n/a	chr19:19101367-19101375
16	POLR2A	chr19:19100090-19101643	A549	lung:	n/a	n/a
17	POLR2A	chr19:19100961-19101569	K562	blood:	n/a	n/a
18	POLR2A	chr19:19100966-19101287	HCT-116	colon:	n/a	n/a
19	POLR2A	chr19:19100530-19101696	K562	blood:	n/a	n/a
20	POLR2A	chr19:19100496-19101706	K562	blood:	n/a	n/a
21	NFATC1	chr19:19100820-19101283	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:19100011-19101562	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr19:19100907-19101225	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:19100598-19101637	K562	blood:	n/a	n/a
25	CCNT2	chr19:19100913-19101354	K562	blood:	n/a	chr19:19101304-19101313
26	POLR2A	chr19:19101109-19101262	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:19100525-19101612	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:19100068-19101488	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr19:19100540-19101737	GM12891	blood:	n/a	n/a
30	ZMIZ1	chr19:19101174-19101374	K562	blood:	n/a	n/a
31	POLR2A	chr19:19100191-19101461	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:19100823-19101432	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr19:19101148-19101484	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr19:19100623-19101523	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:19100000-19101464	U87	brain:	n/a	n/a
36	MTA3	chr19:19099927-19101533	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:19100795-19101634	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:19099930-19101770	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr19:19101118-19101404	HepG2	liver:	n/a	n/a
40	POLR2A	chr19:19100088-19102888	K562	blood:	n/a	n/a
41	PML	chr19:19100257-19101453	GM12878	blood:	n/a	chr19:19101182-19101190
42	POLR2A	chr19:19100114-19101675	GM12891	blood:	n/a	n/a
43	POLR2A	chr19:19100837-19101764	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr19:19100806-19101314	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr19:19100833-19101459	GM12892	blood:	n/a	n/a
46	POLR2A	chr19:19100283-19102204	HL-60	blood:	n/a	n/a
47	POLR2A	chr19:19100780-19101701	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr19:19100059-19101646	PFSK-1	brain:	n/a	n/a
49	STAT5A	chr19:19100398-19101320	GM12878	blood:	n/a	chr19:19100767-19100775 chr19:19101068-19101080
50	POLR2A	chr19:19100049-19101659	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19099305..19102487-chr19:19102568..19107094,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269131	TF binding region
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404020	0.83[AFR][1000 genomes]
rs10404077	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405178	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405609	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406282	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	0.93[AFR][1000 genomes]
rs10407980	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409265	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10409395	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411413	1.00[YRI][hapmap]
rs10411786	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10412101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415998	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs10416041	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418688	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420559	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422238	0.84[AFR][1000 genomes]
rs10422813	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10426131	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13344835	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs28369262	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28421315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28475392	0.83[AFR][1000 genomes]
rs28477157	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	1.00[AFR][1000 genomes]
rs28507927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28533991	0.86[AFR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28582808	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28619464	0.95[AFR][1000 genomes]
rs28628081	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28699197	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs28720008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35646935	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252085	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7256152	1.00[EUR][1000 genomes]
rs8106189	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9917000	1.00[EUR][1000 genomes]
rs9917034	1.00[EUR][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	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19084200-19107800	Weak transcription	Right Atrium	heart
2	chr19:19096200-19101600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr19:19096200-19104000	Weak transcription	Primary B cells from cord blood	blood
4	chr19:19096400-19102200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:19096400-19103400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:19096400-19103600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr19:19096600-19101400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:19096600-19103400	Weak transcription	NH-A	brain
9	chr19:19096800-19102400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:19096800-19104000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:19097000-19101800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:19097600-19101800	Weak transcription	NHLF	lung
13	chr19:19097600-19102000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:19097600-19102400	Weak transcription	Left Ventricle	heart
15	chr19:19097600-19103400	Weak transcription	HUVEC	blood vessel
16	chr19:19097600-19103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:19098000-19101400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr19:19098000-19101400	Weak transcription	Liver	Liver
19	chr19:19098000-19101400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:19098000-19101400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr19:19098000-19101400	Weak transcription	NHDF-Ad	bronchial
22	chr19:19098000-19101600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:19098000-19101800	Weak transcription	Fetal Brain Male	brain
24	chr19:19098000-19101800	Weak transcription	Pancreas	Pancrea
25	chr19:19098000-19101800	Weak transcription	HMEC	breast
26	chr19:19098000-19102000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:19098000-19102000	Weak transcription	Brain Angular Gyrus	brain
28	chr19:19098000-19102000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:19098000-19102000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr19:19098000-19102000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:19098000-19102200	Weak transcription	Gastric	stomach
32	chr19:19098000-19102400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:19098000-19102400	Weak transcription	A549	lung
34	chr19:19098000-19103400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:19098000-19103600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:19098000-19103600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:19098000-19103600	Weak transcription	Hela-S3	cervix
38	chr19:19098000-19103800	Weak transcription	NHEK	skin
39	chr19:19098000-19106600	Weak transcription	Fetal Kidney	kidney
40	chr19:19098200-19102000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr19:19098200-19103400	Weak transcription	K562	blood
42	chr19:19098200-19104600	Weak transcription	Stomach Mucosa	stomach
43	chr19:19098400-19103600	Weak transcription	HepG2	liver
44	chr19:19098600-19101400	Weak transcription	Osteobl	bone
45	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr19:19098800-19103400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:19099000-19103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:19099000-19103400	Weak transcription	HSMMtube	muscle
49	chr19:19099000-19103600	Weak transcription	HSMM	muscle
50	chr19:19099200-19101400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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