Variant report

Variant	rs56388054
Chromosome Location	chr19:39837567-39837568
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39834979..39837753-chr19:39902595..39905469,2	MCF-7	breast:
2	chr19:39836209..39838798-chr19:39898622..39900685,2	K562	blood:
3	chr19:39831061..39834961-chr19:39835519..39840001,9	MCF-7	breast:
4	chr19:39836588..39838326-chr19:39882072..39883751,2	K562	blood:
5	chr19:39835229..39838232-chr19:39847109..39849134,3	MCF-7	breast:
6	chr19:39830889..39835466-chr19:39836647..39841099,6	MCF-7	breast:
7	chr19:39836712..39838528-chr19:39893059..39894655,2	K562	blood:
8	chr19:39690001..39692280-chr19:39837485..39839141,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266559	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000090924	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs55874141	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56190851	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57850430	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7253610	1.00[ASN][1000 genomes]
rs7253980	1.00[ASN][1000 genomes]
rs73546046	0.83[EUR][1000 genomes]
rs73546050	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73546077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73546088	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73547912	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73930730	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101598	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8101786	1.00[ASN][1000 genomes]
rs8102889	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
4	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
6	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834000-39842400	Weak transcription	Gastric	stomach
2	chr19:39834200-39838400	Weak transcription	Ovary	ovary
3	chr19:39834200-39846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:39834400-39837600	Weak transcription	NH-A	brain
6	chr19:39834400-39838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:39834400-39838200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr19:39834400-39838400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:39834400-39839800	Enhancers	Fetal Heart	heart
10	chr19:39834400-39840600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:39834400-39841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:39834400-39841800	Weak transcription	Lung	lung
13	chr19:39834400-39842000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:39834400-39842000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:39834400-39842000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:39834400-39842200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:39834400-39842200	Weak transcription	Esophagus	oesophagus
18	chr19:39834400-39842400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:39834400-39844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:39834400-39845400	Weak transcription	Fetal Kidney	kidney
21	chr19:39834400-39849200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr19:39834600-39838200	Weak transcription	Fetal Intestine Large	intestine
23	chr19:39834600-39838600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:39834600-39838600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:39834600-39838600	Weak transcription	NHEK	skin
26	chr19:39834600-39838800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:39834600-39842400	Weak transcription	Colonic Mucosa	Colon
28	chr19:39834600-39842400	Weak transcription	HMEC	breast
29	chr19:39834800-39837800	Weak transcription	HUVEC	blood vessel
30	chr19:39834800-39838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:39834800-39839000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:39834800-39839200	Genic enhancers	Brain Hippocampus Middle	brain
33	chr19:39834800-39842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:39834800-39847400	Weak transcription	Small Intestine	intestine
35	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39835000-39838000	Weak transcription	Liver	Liver
39	chr19:39835000-39838200	Weak transcription	Hela-S3	cervix
40	chr19:39835000-39844600	Weak transcription	Stomach Mucosa	stomach
41	chr19:39835000-39846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:39835200-39838000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:39835200-39839200	Genic enhancers	Dnd41	blood
44	chr19:39835400-39838000	Weak transcription	Thymus	Thymus
45	chr19:39835400-39839200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:39835400-39839800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr19:39835600-39838000	Strong transcription	A549	lung
48	chr19:39835600-39838200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr19:39835600-39838600	Genic enhancers	NHLF	lung
50	chr19:39835600-39839200	Enhancers	Right Atrium	heart

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