Variant report

Variant	rs11878466
Chromosome Location	chr19:40952884-40952885
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40951476-40953015	K562	blood:	n/a	n/a
2	POLR2A	chr19:40944883-40955137	K562	blood:	n/a	n/a
3	BCL3	chr19:40951484-40952923	A549	lung:	n/a	chr19:40951924-40951933
4	POLR2A	chr19:40952648-40952929	K562	blood:	n/a	n/a
5	POLR2A	chr19:40951489-40952948	K562	blood:	n/a	n/a
6	POLR2A	chr19:40951475-40953099	PBDE	blood:	n/a	n/a
7	POLR2A	chr19:40951158-40953310	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40929000..40933496-chr19:40948111..40953156,29	MCF-7	breast:
2	chr19:40952414..40954708-chr19:40961386..40963710,2	K562	blood:
3	chr19:40948595..40953789-chr19:40967165..40973013,15	MCF-7	breast:
4	chr19:40947599..40953337-chr19:40966407..40973377,15	K562	blood:
5	chr19:40951142..40953802-chr19:40962928..40965821,2	MCF-7	breast:
6	chr19:40942505..40944262-chr19:40952236..40954186,2	K562	blood:
7	chr19:40929942..40935093-chr19:40947472..40955743,23	K562	blood:
8	chr19:40945484..40955522-chr19:40966442..40973559,31	MCF-7	breast:
9	chr19:40947836..40953426-chr19:40969681..40973823,16	K562	blood:
10	chr19:40925098..40933993-chr19:40944045..40956524,41	K562	blood:
11	chr19:40919789..40935162-chr19:40946854..40955873,58	MCF-7	breast:

No data

Variant related genes	Relation type
SERTAD3	TF binding region
ENSG00000090013	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000160460	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28427504	0.83[AMR][1000 genomes]
rs28529139	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56307925	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7256097	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73559683	0.90[AMR][1000 genomes];1.00[EUR][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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
6	nsv911709	chr19:40928944-41060616	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40950600-40953600	Weak transcription	Gastric	stomach
2	chr19:40950600-40953600	Weak transcription	Spleen	Spleen
3	chr19:40951000-40953200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr19:40951000-40953600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:40951000-40953600	Weak transcription	Esophagus	oesophagus
6	chr19:40951000-40953600	Weak transcription	Left Ventricle	heart
7	chr19:40951000-40953600	Weak transcription	Lung	lung
8	chr19:40951000-40953600	Weak transcription	Ovary	ovary
9	chr19:40951000-40953600	Weak transcription	Pancreas	Pancrea
10	chr19:40951000-40953600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:40951000-40970200	Weak transcription	Small Intestine	intestine
12	chr19:40951000-40970400	Weak transcription	Fetal Heart	heart
13	chr19:40951000-40970600	Weak transcription	Psoas Muscle	Psoas
14	chr19:40951000-40971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr19:40951200-40953600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:40951200-40953600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr19:40951200-40953600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:40951200-40953600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:40951200-40953600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:40951200-40953600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:40951200-40953600	Weak transcription	Adipose Nuclei	Adipose
22	chr19:40951200-40953600	Weak transcription	Aorta	Aorta
23	chr19:40951200-40953600	Weak transcription	Brain Anterior Caudate	brain
24	chr19:40951200-40953600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:40951200-40953600	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:40951200-40953600	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:40951200-40953600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:40951200-40953600	Weak transcription	Fetal Lung	lung
29	chr19:40951200-40953600	Weak transcription	Right Ventricle	heart
30	chr19:40951200-40953600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:40951200-40953600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:40951200-40953800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:40951200-40953800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr19:40951200-40954000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:40951200-40954200	Weak transcription	Brain Germinal Matrix	brain
36	chr19:40951200-40954400	Weak transcription	HSMM	muscle
37	chr19:40951200-40956200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:40951200-40956800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:40951200-40957200	Weak transcription	Primary B cells from cord blood	blood
40	chr19:40951200-40957600	Weak transcription	Primary T cells from cord blood	blood
41	chr19:40951200-40957800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:40951200-40961200	Weak transcription	Thymus	Thymus
43	chr19:40951200-40967000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:40951200-40969000	Weak transcription	NHDF-Ad	bronchial
45	chr19:40951200-40969800	Weak transcription	Right Atrium	heart
46	chr19:40951200-40970400	Weak transcription	Brain Angular Gyrus	brain
47	chr19:40951200-40970400	Weak transcription	Brain Substantia Nigra	brain
48	chr19:40951200-40970400	Weak transcription	HSMMtube	muscle
49	chr19:40951200-40970400	Weak transcription	NH-A	brain
50	chr19:40951200-40970600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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