Variant report

Variant	rs12609401
Chromosome Location	chr19:39522337-39522338
allele	A/C
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	NRF1	chr19:39521963-39523086	SK-N-SH	brain:	n/a	chr19:39522088-39522097
2	POLR2A	chr19:39522084-39522802	A549	lung:	n/a	n/a
3	MAX	chr19:39521716-39522972	ECC-1	luminal epithelium:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
4	HEY1	chr19:39522305-39522728	K562	blood:	n/a	n/a
5	MAX	chr19:39521799-39522928	SK-N-SH	brain:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
6	POLR2A	chr19:39522299-39522784	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr19:39521757-39522618	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:39521596-39522804	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD1	chr19:39521887-39522458	GM12878	blood:	n/a	n/a
10	NFIC	chr19:39522314-39523139	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr19:39521624-39523805	K562	blood:	n/a	n/a
12	HEY1	chr19:39521569-39522428	HepG2	liver:	n/a	n/a
13	MAZ	chr19:39521799-39522518	Hela-S3	cervix:	n/a	chr19:39522034-39522044 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522039-39522050 chr19:39522041-39522048
14	POLR2A	chr19:39522268-39522883	Gliobla	brain:	n/a	n/a
15	BHLHE40	chr19:39521844-39522426	GM12878	blood:	n/a	n/a
16	E2F6	chr19:39522175-39522941	K562	blood:	n/a	n/a
17	USF1	chr19:39521624-39522724	A549	lung:	n/a	chr19:39522063-39522074
18	CHD2	chr19:39522159-39522540	GM12878	blood:	n/a	n/a
19	ZEB1	chr19:39522074-39522594	GM12878	blood:	n/a	n/a
20	MAX	chr19:39521801-39522953	MCF-7	breast:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
21	RCOR1	chr19:39521822-39522658	K562	blood:	n/a	n/a
22	MAX	chr19:39521563-39523097	A549	lung:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
23	MAX	chr19:39521740-39522810	A549	lung:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522039-39522050 chr19:39522041-39522048
24	MAX	chr19:39521687-39522911	ECC-1	luminal epithelium:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
25	JUND	chr19:39522002-39522737	A549	lung:	n/a	n/a
26	SP4	chr19:39522108-39522695	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:39522298-39522718	K562	blood:	n/a	n/a
28	TCF12	chr19:39522172-39522918	ECC-1	luminal epithelium:	n/a	n/a
29	ATF3	chr19:39521668-39522849	A549	lung:	n/a	chr19:39522088-39522097
30	MAX	chr19:39521816-39522817	SK-N-SH	brain:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522039-39522050 chr19:39522041-39522048
31	HMGN3	chr19:39521934-39523312	K562	blood:	n/a	n/a
32	MXI1	chr19:39521765-39522542	GM12878	blood:	n/a	n/a
33	ZBTB7A	chr19:39522212-39523126	ECC-1	luminal epithelium:	n/a	n/a
34	MAX	chr19:39521929-39522649	MCF-7	breast:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522039-39522050 chr19:39522041-39522048
35	POLR2A	chr19:39521677-39522761	K562	blood:	n/a	n/a
36	ELF1	chr19:39522027-39522851	MCF-7	breast:	n/a	chr19:39522482-39522493 chr19:39522480-39522493
37	HDAC2	chr19:39522039-39522884	MCF-7	breast:	n/a	n/a
38	REST	chr19:39521494-39522856	A549	lung:	n/a	n/a
39	GATA3	chr19:39522096-39522794	MCF-7	breast:	n/a	n/a
40	USF1	chr19:39521736-39522491	A549	lung:	n/a	chr19:39522063-39522074
41	GABPA	chr19:39522284-39522677	A549	lung:	n/a	n/a
42	NR2F2	chr19:39521704-39522386	K562	blood:	n/a	n/a
43	CEBPD	chr19:39522066-39522475	HepG2	liver:	n/a	n/a
44	MAX	chr19:39521749-39522773	GM12878	blood:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522039-39522050 chr19:39522041-39522048
45	ELF1	chr19:39521765-39522777	GM12878	blood:	n/a	chr19:39522482-39522493 chr19:39522480-39522493
46	POLR2A	chr19:39522299-39522788	SK-N-SH	brain:	n/a	n/a
47	ZBTB7A	chr19:39522125-39523041	ECC-1	luminal epithelium:	n/a	n/a
48	SIN3AK20	chr19:39521478-39523896	PANC-1	pancreas:	n/a	n/a
49	MAX	chr19:39521862-39523558	H1-hESC	embryonic stem cell:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
50	MAX	chr19:39521731-39522424	Hela-S3	cervix:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522039-39522050 chr19:39522041-39522048

No.	Distal block	Cell Line	Cell type
1	chr19:39464957..39467280-chr19:39522120..39523795,2	K562	blood:
2	chr19:39464164..39468178-chr19:39520932..39524285,4	MCF-7	breast:
3	chr19:39521357..39523979-chr19:39614875..39616703,2	MCF-7	breast:

Variant related genes	Relation type
FBXO27	TF binding region
ENSG00000269190	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10409280	0.82[ASN][1000 genomes]
rs10411234	0.90[ASN][1000 genomes]
rs12463075	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12974080	0.89[ASN][1000 genomes]
rs12974708	0.82[ASN][1000 genomes]
rs12975482	0.83[ASN][1000 genomes]
rs12976100	0.82[ASN][1000 genomes]
rs12979968	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12981133	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12981826	0.85[EUR][1000 genomes]
rs12982067	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12983352	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12984833	0.81[ASN][1000 genomes]
rs12984836	0.81[ASN][1000 genomes]
rs1626050	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1627631	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1628376	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1628426	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1629253	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1651747	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16973058	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1864186	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864188	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1869982	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34240661	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34366439	0.84[EUR][1000 genomes]
rs35000840	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35622111	0.91[ASN][1000 genomes]
rs35940388	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4381706	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4511651	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4802010	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487356	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs516901	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs523890	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs523943	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs542464	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553330	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs554932	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs561148	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561329	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs572764	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57401831	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57588219	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57724551	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582575	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582593	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs583529	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs583995	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs584806	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs584822	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs586107	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs586176	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59698424	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs598468	0.90[ASN][1000 genomes]
rs599230	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602899	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61553368	0.93[ASN][1000 genomes]
rs618068	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62119464	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62119508	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62119510	0.92[ASN][1000 genomes]
rs62121528	0.84[EUR][1000 genomes]
rs62121529	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62121530	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62121531	0.81[ASN][1000 genomes]
rs62121532	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662202	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs667911	0.81[EUR][1000 genomes]
rs678772	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs678848	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs679657	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs679732	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7246076	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930100	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12609401	FBXO27	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39521000-39523600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:39521200-39522600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
3	chr19:39521400-39522400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:39521400-39523600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:39521400-39523600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:39521400-39523800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:39521600-39522600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
8	chr19:39521600-39522600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
9	chr19:39521600-39522800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:39521600-39522800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
11	chr19:39521600-39522800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
12	chr19:39521600-39522800	Active TSS	NHDF-Ad	bronchial
13	chr19:39521600-39523000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:39521600-39523200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:39521600-39523200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:39521600-39523400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:39521600-39523600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr19:39521600-39523600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:39521600-39523600	Active TSS	Rectal Smooth Muscle	rectum
20	chr19:39521600-39523800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:39521600-39523800	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr19:39521800-39522400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:39521800-39522400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:39521800-39522400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
25	chr19:39521800-39522400	Flanking Active TSS	Placenta	Placenta
26	chr19:39521800-39522600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
27	chr19:39521800-39522600	Active TSS	Fetal Kidney	kidney
28	chr19:39521800-39522800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:39521800-39522800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:39521800-39522800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:39521800-39522800	Flanking Active TSS	Right Ventricle	heart
32	chr19:39521800-39522800	Active TSS	A549	lung
33	chr19:39521800-39522800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr19:39521800-39523000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:39521800-39523000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:39521800-39523000	Active TSS	Pancreas	Pancrea
37	chr19:39521800-39523200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:39521800-39523200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr19:39521800-39523200	Active TSS	Fetal Intestine Large	intestine
40	chr19:39521800-39523200	Transcr. at gene 5' and 3'	Right Atrium	heart
41	chr19:39521800-39523200	Active TSS	HSMM	muscle
42	chr19:39521800-39523400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:39521800-39523400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr19:39521800-39523400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:39521800-39523400	Active TSS	Brain Substantia Nigra	brain
46	chr19:39521800-39523400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr19:39521800-39523400	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr19:39521800-39523400	Active TSS	HepG2	liver
49	chr19:39521800-39523600	Active TSS	H9 Cell Line	embryonic stem cell
50	chr19:39521800-39523600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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