Variant report

Variant	rs12462170
Chromosome Location	chr19:39403637-39403638
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr19:39403575-39403992	GM12878	blood:	n/a	n/a
2	SPI1	chr19:39403621-39404043	GM12891	blood:	n/a	n/a
3	RUNX3	chr19:39403463-39403861	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39403081-39404054	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:39403240-39403637	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr19:39402962-39404270	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:39403594-39403878	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:39403623-39403834	A549	lung:	n/a	n/a
9	POLR2A	chr19:39402959-39404002	H1-hESC	embryonic stem cell:	n/a	n/a
10	RUNX3	chr19:39403537-39403851	GM12878	blood:	n/a	n/a
11	BCL3	chr19:39403038-39404108	A549	lung:	n/a	n/a
12	EGR1	chr19:39403600-39403754	GM12878	blood:	n/a	chr19:39403658-39403672
13	EGR1	chr19:39403564-39403814	K562	blood:	n/a	chr19:39403658-39403672
14	POLR2A	chr19:39403155-39404173	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr19:39403112-39404338	K562	blood:	n/a	n/a
16	POLR2A	chr19:39403299-39404105	K562	blood:	n/a	n/a
17	POLR2A	chr19:39403536-39403834	HepG2	liver:	n/a	n/a
18	EBF1	chr19:39403588-39403881	GM12878	blood:	n/a	n/a
19	SPI1	chr19:39403592-39404185	HL-60	blood:	n/a	n/a
20	POLR2A	chr19:39402657-39410674	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr19:39403173-39403968	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr19:39403246-39404111	HL-60	blood:	n/a	n/a
23	POLR2A	chr19:39402636-39404193	K562	blood:	n/a	n/a
24	POLR2A	chr19:39403006-39404106	K562	blood:	n/a	n/a
25	POLR2A	chr19:39403396-39403979	A549	lung:	n/a	n/a
26	POLR2A	chr19:39399024-39410741	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr19:39403595-39403802	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39388933..39390518-chr19:39401475..39404370,2	MCF-7	breast:
2	chr19:39390131..39392480-chr19:39402477..39404053,2	MCF-7	breast:
3	chr19:39384229..39386196-chr19:39403385..39405980,2	K562	blood:
4	chr19:39398169..39400794-chr19:39403289..39404909,2	MCF-7	breast:
5	chr19:39402244..39405531-chr19:39405569..39407779,3	MCF-7	breast:

No data

Variant related genes	Relation type
CCER2	TF binding region
ENSG00000068903	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000104825	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10412886	0.95[ASN][1000 genomes]
rs10415194	0.99[ASN][1000 genomes]
rs11882588	0.84[ASN][1000 genomes]
rs12460327	0.98[ASN][1000 genomes]
rs2099339	0.90[ASN][1000 genomes]
rs2288855	0.89[ASN][1000 genomes]
rs28375245	0.92[ASN][1000 genomes]
rs3136645	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4801945	0.91[ASN][1000 genomes]
rs751941	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911677	chr19:39395654-39404457	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391600-39414800	Weak transcription	HMEC	breast
3	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
4	chr19:39391800-39412200	Weak transcription	Osteobl	bone
5	chr19:39392400-39414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:39392600-39406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:39392600-39414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:39395600-39414800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:39395600-39415000	Weak transcription	Hela-S3	cervix
11	chr19:39396600-39408400	Weak transcription	HepG2	liver
12	chr19:39396800-39412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:39397000-39412200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:39398000-39412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
16	chr19:39398200-39412200	Weak transcription	Brain Angular Gyrus	brain
17	chr19:39398400-39411600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:39398600-39410200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:39398600-39415000	Weak transcription	Brain Substantia Nigra	brain
20	chr19:39398800-39403800	Weak transcription	HSMM	muscle
21	chr19:39398800-39409000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr19:39398800-39410000	Weak transcription	HSMMtube	muscle
23	chr19:39398800-39411600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:39398800-39412000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr19:39398800-39412200	Weak transcription	NHEK	skin
26	chr19:39398800-39412400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:39398800-39415000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:39399000-39412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:39399800-39408400	Weak transcription	A549	lung
30	chr19:39399800-39409000	Weak transcription	Pancreas	Pancrea
31	chr19:39399800-39412200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:39399800-39412200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr19:39399800-39414800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr19:39399800-39414800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:39400000-39405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:39400000-39405800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:39400000-39405800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr19:39400000-39410000	Weak transcription	K562	blood
39	chr19:39400000-39412000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr19:39400000-39412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:39400000-39412200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:39400000-39412200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr19:39400000-39412200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:39400000-39414200	Weak transcription	Left Ventricle	heart
45	chr19:39400200-39404600	Weak transcription	Spleen	Spleen
46	chr19:39400200-39405800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:39400200-39405800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:39400200-39405800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:39400200-39405800	Weak transcription	Liver	Liver
50	chr19:39400200-39405800	Weak transcription	Lung	lung

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