Variant report

Variant	rs11538454
Chromosome Location	chr19:36549690-36549691
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr19:36549569-36550278	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:36549631-36550404	HepG2	liver:	n/a	n/a
3	MAX	chr19:36549620-36550050	HepG2	liver:	n/a	n/a
4	HNF4A	chr19:36549609-36550223	HepG2	liver:	n/a	chr19:36550028-36550043
5	MAX	chr19:36549394-36550312	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:36549682-36550326	HepG2	liver:	n/a	n/a
7	HDAC2	chr19:36549578-36550206	HepG2	liver:	n/a	chr19:36549779-36549788
8	TEAD4	chr19:36549540-36550262	HepG2	liver:	n/a	n/a
9	ZEB1	chr19:36549342-36550469	HepG2	liver:	n/a	chr19:36550023-36550034
10	MAX	chr19:36549437-36550350	HepG2	liver:	n/a	n/a
11	MXI1	chr19:36549589-36550190	HepG2	liver:	n/a	n/a
12	EP300	chr19:36549660-36550191	HepG2	liver:	n/a	n/a
13	MYBL2	chr19:36549625-36550259	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:36548167..36550367-chr19:36618997..36621964,2	MCF-7	breast:
2	chr19:36544812..36547842-chr19:36549137..36553614,5	MCF-7	breast:
3	chr19:36484438..36486588-chr19:36547484..36549798,2	K562	blood:
4	chr19:36548716..36551375-chr19:36610382..36612902,2	MCF-7	breast:
5	chr19:36543835..36550918-chr19:36603651..36608049,11	MCF-7	breast:
6	chr19:36539473..36542401-chr19:36548947..36550906,2	K562	blood:
7	chr19:36498186..36501262-chr19:36549375..36551600,3	MCF-7	breast:

No data

Variant related genes	Relation type
THAP8	TF binding region
ENSG00000105254	Chromatin interaction
ENSG00000161277	Chromatin interaction
ENSG00000181392	Chromatin interaction
ENSG00000205138	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000105261	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1009381	0.85[ASN][1000 genomes]
rs10406862	0.88[ASN][1000 genomes]
rs10419924	0.86[ASN][1000 genomes]
rs10420345	0.89[ASN][1000 genomes]
rs10421377	0.83[ASN][1000 genomes]
rs10422055	0.87[ASN][1000 genomes]
rs10425700	0.88[ASN][1000 genomes]
rs10427033	0.89[ASN][1000 genomes]
rs11666192	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11669890	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12608517	1.00[ASN][1000 genomes]
rs2023866	0.88[ASN][1000 genomes]
rs2074435	0.85[ASN][1000 genomes]
rs2075472	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2141959	0.86[ASN][1000 genomes]
rs2301734	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301737	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2871649	1.00[ASN][1000 genomes]
rs4555271	0.86[ASN][1000 genomes]
rs4806249	0.85[ASN][1000 genomes]
rs4806254	0.80[ASN][1000 genomes]
rs4806262	0.89[ASN][1000 genomes]
rs4806271	0.90[ASN][1000 genomes]
rs4806273	0.85[ASN][1000 genomes]
rs4806276	0.93[ASN][1000 genomes]
rs55849299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250364	0.95[ASN][1000 genomes]
rs7251912	0.88[ASN][1000 genomes]
rs7257026	0.81[ASN][1000 genomes]
rs7258807	0.95[ASN][1000 genomes]
rs73036134	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8112640	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
2	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
3	chr19:36546600-36551000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:36546600-36551200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:36546600-36551200	Weak transcription	Brain Substantia Nigra	brain
6	chr19:36546600-36551600	Weak transcription	Brain Angular Gyrus	brain
7	chr19:36546600-36551600	Weak transcription	Brain Anterior Caudate	brain
8	chr19:36546600-36551600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:36546600-36556600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:36546600-36556800	Weak transcription	Spleen	Spleen
11	chr19:36546600-36557800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:36546600-36572400	Weak transcription	Lung	lung
13	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
14	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:36546800-36550000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:36546800-36551600	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:36546800-36551800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:36546800-36551800	Weak transcription	HSMM	muscle
19	chr19:36546800-36557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:36546800-36572000	Weak transcription	Primary T cells from cord blood	blood
21	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
22	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
24	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr19:36547000-36561200	Weak transcription	NH-A	brain
28	chr19:36547200-36557600	Weak transcription	Placenta	Placenta
29	chr19:36547400-36551200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:36547400-36561200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr19:36547400-36562000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:36547600-36549800	Weak transcription	GM12878-XiMat	blood
33	chr19:36547600-36550800	Weak transcription	NHLF	lung
34	chr19:36547600-36553400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:36547600-36553600	Weak transcription	Fetal Lung	lung
36	chr19:36547600-36555800	Weak transcription	HMEC	breast
37	chr19:36547600-36559200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:36547600-36559200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
40	chr19:36547800-36550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:36547800-36552400	Weak transcription	Fetal Brain Female	brain
42	chr19:36547800-36555800	Weak transcription	NHDF-Ad	bronchial
43	chr19:36548000-36549800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:36548000-36550800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:36548000-36559200	Strong transcription	Fetal Thymus	thymus
46	chr19:36548200-36550400	Weak transcription	Brain Germinal Matrix	brain
47	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr19:36548400-36550200	Genic enhancers	Dnd41	blood
49	chr19:36548400-36552600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:36548400-36559200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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