Variant report

Variant	rs73549906
Chromosome Location	chr19:39930812-39930813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39930298-39932492	A549	lung:	n/a	n/a
2	RAD21	chr19:39930288-39931446	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
4	RAD21	chr19:39930701-39931375	HCT-116	colon:	n/a	n/a
5	RAD21	chr19:39930797-39931336	A549	lung:	n/a	n/a
6	RAD21	chr19:39930617-39931447	A549	lung:	n/a	n/a
7	POU2F2	chr19:39930802-39931299	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:39930810-39931288	MCF10A-Er-Src	breast:	n/a	n/a
9	POU2F2	chr19:39930761-39931286	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
11	CTCF	chr19:39930654-39931552	SK-N-SH	brain:	n/a	n/a
12	RAD21	chr19:39930799-39931489	HCT-116	colon:	n/a	n/a
13	FOXA2	chr19:39930732-39931006	HepG2	liver:	n/a	n/a
14	SIX5	chr19:39930400-39931361	A549	lung:	n/a	n/a
15	CEBPZ	chr19:39930811-39931024	HepG2	liver:	n/a	n/a
16	CTCF	chr19:39930786-39931457	HCT-116	colon:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39930044..39931944-chr19:39980921..39983797,2	MCF-7	breast:
2	chr19:39930639..39932223-chr19:40029894..40032497,2	MCF-7	breast:
3	chr19:39930627..39931572-chr19:40023181..40024237,5	K562	blood:
4	chr19:39930777..39932408-chr19:40023425..40025081,2	K562	blood:
5	chr19:39930372..39932549-chr19:39934536..39937097,4	K562	blood:
6	chr19:39930426..39932115-chr19:39937018..39938757,2	MCF-7	breast:

No data

Variant related genes	Relation type
RPS16	TF binding region
SUPT5H	TF binding region
ENSG00000176396	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10413140	1.00[AMR][1000 genomes]
rs13346052	1.00[AMR][1000 genomes]
rs61569178	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547970	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547976	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547991	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547993	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547999	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549905	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549912	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549922	1.00[AMR][1000 genomes]
rs73549928	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549930	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549931	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551806	1.00[AMR][1000 genomes]
rs73551815	1.00[AMR][1000 genomes]
rs73551829	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551839	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551844	1.00[AMR][1000 genomes]
rs7359872	0.84[AFR][1000 genomes];1.00[AMR][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	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
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39926600-39935200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:39927400-39935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39927400-39935200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:39927400-39935200	Weak transcription	Gastric	stomach
5	chr19:39927400-39935200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:39927600-39931000	Weak transcription	Primary B cells from cord blood	blood
7	chr19:39927600-39931000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr19:39927600-39931000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:39927600-39931000	Weak transcription	Liver	Liver
10	chr19:39927600-39931000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:39927600-39931000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:39927600-39932000	Enhancers	A549	lung
13	chr19:39927600-39934800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:39927600-39935000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr19:39927600-39935000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:39927600-39935000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:39927600-39935000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:39927600-39935000	Weak transcription	HMEC	breast
19	chr19:39927600-39935200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr19:39927600-39935200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:39927600-39935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:39927600-39935200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:39927600-39935200	Weak transcription	Brain Anterior Caudate	brain
24	chr19:39927600-39935200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:39927600-39935200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr19:39927600-39935200	Weak transcription	Fetal Kidney	kidney
27	chr19:39927600-39935200	Weak transcription	HSMMtube	muscle
28	chr19:39927600-39935200	Weak transcription	NHLF	lung
29	chr19:39927800-39931000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:39927800-39931000	Weak transcription	Dnd41	blood
31	chr19:39927800-39931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:39928600-39935000	Weak transcription	Fetal Intestine Small	intestine
33	chr19:39929200-39932000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:39929200-39932200	Enhancers	HepG2	liver
35	chr19:39929400-39931200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:39929400-39935000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:39929400-39935000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr19:39929600-39931000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:39929800-39934000	Weak transcription	Placenta	Placenta
40	chr19:39929800-39935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:39929800-39935000	Weak transcription	NHEK	skin
42	chr19:39930000-39931400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:39930200-39932000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:39930400-39931000	Enhancers	K562	blood
45	chr19:39930400-39932400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:39930600-39931000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:39930600-39931200	Enhancers	GM12878-XiMat	blood
48	chr19:39930600-39932000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:39930600-39935000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39930800-39931000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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