Variant report

Variant	rs13346452
Chromosome Location	chr19:39836800-39836801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39836680-39836830	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr19:39836720-39836870	HPF	lung:	n/a	n/a
3	CTCF	chr19:39836680-39836830	HepG2	liver:	n/a	n/a
4	CTCF	chr19:39836700-39836850	AG10803	skin:	n/a	n/a
5	CTCF	chr19:39836660-39836950	GM12868	blood:	n/a	n/a
6	CTCF	chr19:39836740-39836890	GM12878	blood:	n/a	n/a
7	CTCF	chr19:39836720-39836870	BE2_C	brain:	n/a	n/a
8	CTCF	chr19:39836720-39836870	HFF-Myc	foreskin:	n/a	n/a
9	CTCF	chr19:39836720-39836870	HMF	breast:	n/a	n/a
10	CTCF	chr19:39836660-39836810	GM12864	blood:	n/a	n/a
11	CTCF	chr19:39836720-39836870	HCM	heart:	n/a	n/a
12	CTCF	chr19:39836720-39836870	GM12867	blood:	n/a	n/a
13	CTCF	chr19:39836720-39836870	HMEC	breast:	n/a	n/a
14	CTCF	chr19:39836760-39836910	AG10803	skin:	n/a	n/a
15	CTCF	chr19:39836782-39836859	GM12878	blood:	n/a	n/a
16	CTCF	chr19:39836680-39836830	HFF	foreskin:	n/a	n/a
17	CTCF	chr19:39836680-39836830	BJ	skin:	n/a	n/a
18	CTCF	chr19:39836700-39836850	NHEK	skin:	n/a	n/a
19	CTCF	chr19:39836700-39836850	HPAF	blood vessel:	n/a	n/a
20	CTCF	chr19:39836700-39836850	AG09319	gingival:	n/a	n/a
21	CTCF	chr19:39836800-39836950	HFF-Myc	foreskin:	n/a	n/a
22	CTCF	chr19:39836720-39836870	GM12864	blood:	n/a	n/a
23	CTCF	chr19:39836760-39836910	NB4	blood:	n/a	n/a
24	CTCF	chr19:39836760-39836910	GM12866	blood:	n/a	n/a
25	CTCF	chr19:39836720-39836870	GM12869	blood:	n/a	n/a
26	CTCF	chr19:39836700-39836850	MCF-7	breast:	n/a	n/a
27	CTCF	chr19:39836680-39836830	HAc	cerebellar:	n/a	n/a
28	CTCF	chr19:39836760-39836910	HBMEC	blood vessel:	n/a	n/a
29	CTCF	chr19:39836700-39836850	GM12873	blood:	n/a	n/a
30	CTCF	chr19:39836760-39836910	K562	blood:	n/a	n/a
31	CTCF	chr19:39836720-39836870	HEK293	kidney:	n/a	n/a
32	CTCF	chr19:39836740-39836890	AG04450	lung:	n/a	n/a
33	CTCF	chr19:39836740-39836890	HVMF	connective:	n/a	n/a
34	CTCF	chr19:39836700-39836850	HepG2	liver:	n/a	n/a
35	CTCF	chr19:39836720-39836870	HCPEpiC	choroid plexus:	n/a	n/a
36	CTCF	chr19:39836680-39836830	K562	blood:	n/a	n/a
37	CTCF	chr19:39836680-39836830	NHDF-neo	bronchial:	n/a	n/a
38	CTCF	chr19:39836800-39836950	HRPEpiC	eye:	n/a	n/a
39	CTCF	chr19:39836760-39836910	GM12871	blood:	n/a	n/a
40	CTCF	chr19:39836679-39836921	IMR90	lung:	n/a	n/a
41	CTCF	chr19:39836700-39836850	GM12874	blood:	n/a	n/a
42	CTCF	chr19:39836800-39836950	RPTEC	kidney:	n/a	n/a
43	CTCF	chr19:39836720-39836870	HVMF	connective:	n/a	n/a
44	CTCF	chr19:39836708-39836861	HepG2	liver:	n/a	n/a
45	CTCF	chr19:39836680-39836830	A549	lung:	n/a	n/a
46	CTCF	chr19:39836720-39836870	GM06990	blood:	n/a	n/a
47	CTCF	chr19:39836740-39836890	GM12873	blood:	n/a	n/a
48	CTCF	chr19:39836680-39836830	AG09319	gingival:	n/a	n/a
49	CTCF	chr19:39836680-39836830	GM12875	blood:	n/a	n/a
50	CTCF	chr19:39836660-39836810	GM06990	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39834979..39837753-chr19:39902595..39905469,2	MCF-7	breast:
2	chr19:39834449..39837367-chr19:39853608..39855481,2	K562	blood:
3	chr19:39836209..39838798-chr19:39898622..39900685,2	K562	blood:
4	chr19:39831061..39834961-chr19:39835519..39840001,9	MCF-7	breast:
5	chr19:39835239..39836908-chr19:39924259..39926190,2	MCF-7	breast:
6	chr19:39836588..39838326-chr19:39882072..39883751,2	K562	blood:
7	chr19:39832709..39837239-chr19:39925090..39928725,4	K562	blood:
8	chr19:39835229..39838232-chr19:39847109..39849134,3	MCF-7	breast:
9	chr19:39830889..39835466-chr19:39836647..39841099,6	MCF-7	breast:
10	chr19:39835965..39836894-chr19:39901884..39902780,2	MCF-7	breast:
11	chr19:39830669..39836861-chr19:39895802..39900887,6	MCF-7	breast:
12	chr19:39835028..39836930-chr19:39843586..39846123,3	MCF-7	breast:
13	chr19:39835368..39837206-chr19:39838321..39840003,3	MCF-7	breast:
14	chr19:39836712..39838528-chr19:39893059..39894655,2	K562	blood:

No data

Variant related genes	Relation type
GMFG	TF binding region
ENSG00000269246	TF binding region
SAMD4B	TF binding region
ENSG00000128016	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000130755	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10405369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422570	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422996	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424274	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13344909	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28519468	1.00[EUR][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:141 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834000-39842400	Weak transcription	Gastric	stomach
2	chr19:39834200-39836800	Enhancers	Right Ventricle	heart
3	chr19:39834200-39838400	Weak transcription	Ovary	ovary
4	chr19:39834200-39846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:39834400-39836800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:39834400-39837000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:39834400-39837000	Weak transcription	Fetal Thymus	thymus
9	chr19:39834400-39837200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr19:39834400-39837200	Weak transcription	HSMMtube	muscle
11	chr19:39834400-39837600	Weak transcription	NH-A	brain
12	chr19:39834400-39838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:39834400-39838200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr19:39834400-39838400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:39834400-39839800	Enhancers	Fetal Heart	heart
16	chr19:39834400-39840600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:39834400-39841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:39834400-39841800	Weak transcription	Lung	lung
19	chr19:39834400-39842000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr19:39834400-39842000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:39834400-39842000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:39834400-39842200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:39834400-39842200	Weak transcription	Esophagus	oesophagus
24	chr19:39834400-39842400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:39834400-39844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:39834400-39845400	Weak transcription	Fetal Kidney	kidney
27	chr19:39834400-39849200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr19:39834600-39838200	Weak transcription	Fetal Intestine Large	intestine
29	chr19:39834600-39838600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:39834600-39838600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:39834600-39838600	Weak transcription	NHEK	skin
32	chr19:39834600-39838800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:39834600-39842400	Weak transcription	Colonic Mucosa	Colon
34	chr19:39834600-39842400	Weak transcription	HMEC	breast
35	chr19:39834800-39836800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:39834800-39837000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr19:39834800-39837000	Genic enhancers	Fetal Muscle Leg	muscle
38	chr19:39834800-39837800	Weak transcription	HUVEC	blood vessel
39	chr19:39834800-39838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:39834800-39839000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:39834800-39839200	Genic enhancers	Brain Hippocampus Middle	brain
42	chr19:39834800-39842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:39834800-39847400	Weak transcription	Small Intestine	intestine
44	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:39835000-39836800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:39835000-39836800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:39835000-39837000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr19:39835000-39837000	Genic enhancers	Brain Anterior Caudate	brain

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