Variant report

Variant	rs12983225
Chromosome Location	chr19:40335810-40335811
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:40334506-40337825	A549	lung:	n/a	chr19:40337007-40337014 chr19:40337006-40337015
2	MYC	chr19:40334790-40338257	A549	lung:	n/a	chr19:40337007-40337014 chr19:40337006-40337015
3	POLR2A	chr19:40306432-40338982	PANC-1	pancreas:	n/a	n/a
4	SPI1	chr19:40335678-40336041	GM12891	blood:	n/a	chr19:40335891-40335904 chr19:40335713-40335726
5	CTCF	chr19:40335720-40335870	GM12870	blood:	n/a	n/a
6	SIN3AK20	chr19:40332892-40340524	PANC-1	pancreas:	n/a	n/a
7	WRNIP1	chr19:40334426-40336849	GM12878	blood:	n/a	n/a
8	CTCF	chr19:40334289-40338535	A549	lung:	n/a	chr19:40336774-40336782 chr19:40336634-40336647
9	SIN3AK20	chr19:40334304-40340581	PANC-1	pancreas:	n/a	n/a
10	SPI1	chr19:40335792-40335962	K562	blood:	n/a	chr19:40335891-40335904
11	MXI1	chr19:40334712-40337666	IMR90	lung:	n/a	n/a
12	SPI1	chr19:40335717-40335993	GM12878	blood:	n/a	chr19:40335891-40335904
13	HA-E2F1	chr19:40335730-40336662	MCF-7	breast:	n/a	chr19:40336371-40336378 chr19:40336371-40336378 chr19:40336367-40336379 chr19:40336371-40336378
14	SPI1	chr19:40335614-40336143	HL-60	blood:	n/a	chr19:40335891-40335904 chr19:40335713-40335726
15	ELF1	chr19:40335584-40335957	K562	blood:	n/a	n/a
16	TCF12	chr19:40335468-40337912	A549	lung:	n/a	chr19:40336709-40336717
17	REST	chr19:40334688-40337514	PANC-1	pancreas:	n/a	chr19:40337343-40337363 chr19:40337343-40337363

No.	Distal block	Cell Line	Cell type
1	chr19:40335423..40338376-chr19:40475745..40478585,3	MCF-7	breast:
2	chr19:40322842..40325581-chr19:40335629..40338491,6	MCF-7	breast:
3	chr19:40327506..40332289-chr19:40333216..40337866,9	MCF-7	breast:
4	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
5	chr19:40029325..40030960-chr19:40334605..40336137,2	K562	blood:
6	chr19:40245446..40248757-chr19:40332343..40336010,3	MCF-7	breast:
7	chr19:39926041..39928299-chr19:40334872..40337810,2	MCF-7	breast:
8	chr19:40021563..40023552-chr19:40334495..40337354,2	K562	blood:

Variant related genes	Relation type
FBL	TF binding region
ENSG00000176401	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000269792	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1003947	0.82[ASN][1000 genomes]
rs1003948	0.82[ASN][1000 genomes]
rs10048489	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1017078	0.82[ASN][1000 genomes]
rs1017079	0.82[ASN][1000 genomes]
rs11083539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12972005	0.87[ASN][1000 genomes]
rs12972396	0.87[ASN][1000 genomes]
rs12972914	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12973182	0.82[ASN][1000 genomes]
rs12975231	0.87[ASN][1000 genomes]
rs12976287	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12976359	0.82[ASN][1000 genomes]
rs12979465	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12984432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12984824	0.82[ASN][1000 genomes]
rs12986238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2009348	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2110230	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34308963	0.82[ASN][1000 genomes]
rs34398724	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35390382	0.82[ASN][1000 genomes]
rs35393652	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35488251	0.87[ASN][1000 genomes]
rs35853287	0.82[ASN][1000 genomes]
rs35876606	0.87[ASN][1000 genomes]
rs3760924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3810384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3810385	0.87[ASN][1000 genomes]
rs3944083	0.82[ASN][1000 genomes]
rs6508910	0.82[ASN][1000 genomes]
rs6508911	0.82[ASN][1000 genomes]
rs7251090	0.87[ASN][1000 genomes]
rs7251118	0.87[ASN][1000 genomes]
rs7252906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7258581	0.82[ASN][1000 genomes]
rs7258788	0.82[ASN][1000 genomes]
rs7258881	0.82[ASN][1000 genomes]
rs8102444	0.82[ASN][1000 genomes]
rs8111434	0.82[ASN][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	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40324800-40336000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:40332200-40336000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr19:40332200-40336000	Enhancers	Liver	Liver
4	chr19:40332400-40336000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr19:40333000-40336200	Enhancers	Placenta	Placenta
6	chr19:40333200-40336000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr19:40333200-40336200	Flanking Active TSS	Dnd41	blood
8	chr19:40333400-40336000	Enhancers	Primary B cells from peripheral blood	blood
9	chr19:40333400-40336000	Enhancers	Left Ventricle	heart
10	chr19:40333400-40336600	Enhancers	Spleen	Spleen
11	chr19:40333600-40336200	Weak transcription	Aorta	Aorta
12	chr19:40334000-40336000	Weak transcription	HSMMtube	muscle
13	chr19:40334200-40336000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:40334600-40336000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:40334800-40336000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:40334800-40336000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr19:40334800-40336000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:40334800-40336000	Enhancers	Gastric	stomach
19	chr19:40334800-40336000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr19:40334800-40336000	Enhancers	Right Atrium	heart
21	chr19:40334800-40336000	Enhancers	Small Intestine	intestine
22	chr19:40334800-40336000	Enhancers	Stomach Mucosa	stomach
23	chr19:40334800-40336000	Flanking Active TSS	A549	lung
24	chr19:40334800-40336000	Flanking Active TSS	HepG2	liver
25	chr19:40334800-40336000	Flanking Active TSS	HMEC	breast
26	chr19:40334800-40336200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:40334800-40336200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr19:40334800-40336200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr19:40334800-40336200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:40334800-40336200	Flanking Active TSS	Hela-S3	cervix
31	chr19:40334800-40336200	Flanking Active TSS	NHEK	skin
32	chr19:40334800-40336400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:40334800-40336400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:40334800-40336400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr19:40334800-40336400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr19:40334800-40336600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr19:40334800-40337200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr19:40334800-40337800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:40335000-40336000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:40335000-40336000	Flanking Active TSS	K562	blood
41	chr19:40335000-40337200	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr19:40335200-40336000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:40335200-40336200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:40335200-40336200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:40335200-40336200	Enhancers	Lung	lung
46	chr19:40335200-40336200	Flanking Active TSS	NH-A	brain
47	chr19:40335200-40336600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:40335200-40336600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:40335200-40336600	Flanking Active TSS	HUVEC	blood vessel
50	chr19:40335200-40336800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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