Variant report

Variant	rs636534
Chromosome Location	chr19:39522419-39522420
allele	G/T
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	POLR2A	chr19:39522357-39522620	GM12878	blood:	n/a	n/a
2	NRF1	chr19:39521963-39523086	SK-N-SH	brain:	n/a	chr19:39522088-39522097
3	POLR2A	chr19:39522084-39522802	A549	lung:	n/a	n/a
4	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
5	HEY1	chr19:39522305-39522728	K562	blood:	n/a	n/a
6	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
7	POLR2A	chr19:39522299-39522784	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr19:39521757-39522618	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:39521596-39522804	H1-hESC	embryonic stem cell:	n/a	n/a
10	CHD1	chr19:39521887-39522458	GM12878	blood:	n/a	n/a
11	NFIC	chr19:39522314-39523139	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr19:39521624-39523805	K562	blood:	n/a	n/a
13	HEY1	chr19:39521569-39522428	HepG2	liver:	n/a	n/a
14	REST	chr19:39522377-39522755	ECC-1	luminal epithelium:	n/a	n/a
15	MAZ	chr19:39521799-39522518	Hela-S3	cervix:	n/a	chr19:39522034-39522044 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522039-39522050 chr19:39522041-39522048
16	RUNX3	chr19:39522346-39522660	GM12878	blood:	n/a	n/a
17	CEBPB	chr19:39522396-39522558	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:39522268-39522883	Gliobla	brain:	n/a	n/a
19	BHLHE40	chr19:39521844-39522426	GM12878	blood:	n/a	n/a
20	E2F6	chr19:39522175-39522941	K562	blood:	n/a	n/a
21	USF1	chr19:39521624-39522724	A549	lung:	n/a	chr19:39522063-39522074
22	CHD2	chr19:39522159-39522540	GM12878	blood:	n/a	n/a
23	ZEB1	chr19:39522074-39522594	GM12878	blood:	n/a	n/a
24	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
25	RCOR1	chr19:39521822-39522658	K562	blood:	n/a	n/a
26	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
27	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
28	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
29	JUND	chr19:39522002-39522737	A549	lung:	n/a	n/a
30	SP4	chr19:39522108-39522695	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr19:39522298-39522718	K562	blood:	n/a	n/a
32	TCF12	chr19:39522172-39522918	ECC-1	luminal epithelium:	n/a	n/a
33	ATF3	chr19:39521668-39522849	A549	lung:	n/a	chr19:39522088-39522097
34	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
35	HMGN3	chr19:39521934-39523312	K562	blood:	n/a	n/a
36	MXI1	chr19:39521765-39522542	GM12878	blood:	n/a	n/a
37	SPI1	chr19:39522367-39522604	K562	blood:	n/a	chr19:39522480-39522493 chr19:39522483-39522490 chr19:39522482-39522491
38	ZBTB7A	chr19:39522212-39523126	ECC-1	luminal epithelium:	n/a	n/a
39	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
40	POLR2A	chr19:39521677-39522761	K562	blood:	n/a	n/a
41	ELF1	chr19:39522027-39522851	MCF-7	breast:	n/a	chr19:39522482-39522493 chr19:39522480-39522493
42	HDAC2	chr19:39522039-39522884	MCF-7	breast:	n/a	n/a
43	REST	chr19:39521494-39522856	A549	lung:	n/a	n/a
44	GATA3	chr19:39522096-39522794	MCF-7	breast:	n/a	n/a
45	USF1	chr19:39521736-39522491	A549	lung:	n/a	chr19:39522063-39522074
46	GABPA	chr19:39522284-39522677	A549	lung:	n/a	n/a
47	CEBPD	chr19:39522066-39522475	HepG2	liver:	n/a	n/a
48	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
49	ELF1	chr19:39521765-39522777	GM12878	blood:	n/a	chr19:39522482-39522493 chr19:39522480-39522493
50	POLR2A	chr19:39522299-39522788	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39522418-39522468	H1-hESC	embryonic stem cell:	embryo
2	chr19:39522418-39522468	Jurkat	blood:	n/a
3	chr19:39522418-39522468	NT2-D1	testis:	n/a
4	chr19:39522418-39522468	NHBE	bronchial:	n/a
5	chr19:39522418-39522468	NHDF-neo	bronchial:	n/a
6	chr19:39522418-39522468	PANC-1	pancreas:	n/a
7	chr19:39522418-39522468	Caco-2	colon:	n/a
8	chr19:39522418-39522468	HEK293	kidney:	embryo
9	chr19:39522418-39522468	HPAEpiC	pulmonary alveolar:	n/a
10	chr19:39522418-39522468	CMK	blood:	n/a
11	chr19:39522418-39522468	AG09309	skin:	n/a
12	chr19:39522418-39522468	U87	brain:	n/a
13	chr19:39522418-39522468	HCT-116	colon:	n/a
14	chr19:39522418-39522468	PFSK-1	brain:	n/a
15	chr19:39522418-39522468	HAEpiC	amniotic membrane:	n/a
16	chr19:39522418-39522468	A549	lung:	n/a
17	chr19:39522418-39522468	HNPCEpiC	eye:	n/a
18	chr19:39522418-39522468	RPTEC	kidney:	n/a
19	chr19:39522418-39522468	AG09319	gingival:	n/a
20	chr19:39522418-39522468	GM19239	blood:	n/a
21	chr19:39522418-39522468	LNCaP	prostate:	n/a
22	chr19:39522418-39522468	SK-N-MC	brain:	n/a
23	chr19:39522418-39522468	HL-60	blood:	n/a
24	chr19:39522418-39522468	ovcar-3	ovarian:	n/a
25	chr19:39522418-39522468	Hepatocyte	liver:	n/a
26	chr19:39522418-39522468	SKMC	muscle:	n/a
27	chr19:39522418-39522468	NH-A	brain:	n/a
28	chr19:39522418-39522468	IMR90	lung:	fetal
29	chr19:39522418-39522468	AG04450	lung:	fetal
30	chr19:39522418-39522468	SAEC	small airway:	n/a
31	chr19:39522418-39522468	HepG2	liver:	n/a
32	chr19:39522418-39522468	T-47D	breast:	n/a
33	chr19:39522418-39522468	AG04449	skin:	fetal
34	chr19:39522418-39522468	GM12892	blood:	n/a
35	chr19:39522418-39522468	ProgFib	skin:	n/a
36	chr19:39522418-39522468	SK-N-SH_RA	brain:	n/a
37	chr19:39522418-39522468	K562	blood:	n/a
38	chr19:39522418-39522468	HUVEC	blood vessel:	n/a
39	chr19:39522418-39522468	Hela-S3	cervix:	n/a
40	chr19:39522418-39522468	ECC-1	luminal epithelium:	n/a
41	chr19:39522418-39522468	BJ	skin:	n/a
42	chr19:39522418-39522468	HCPEpiC	choroid plexus:	n/a
43	chr19:39522418-39522468	HRPEpiC	eye:	n/a
44	chr19:39522418-39522468	SK-N-SH	brain:	n/a
45	chr19:39522418-39522468	HMEC	breast:	n/a
46	chr19:39522418-39522468	PrEC	prostate:	n/a
47	chr19:39522418-39522468	HRCEpiC	kidney:	n/a
48	chr19:39522418-39522468	HEEpiC	esophagus:	n/a
49	chr19:39522418-39522468	NB4	blood:	n/a
50	chr19:39522418-39522468	MCF-7	breast:	n/a

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
FBXO27	CpG island
ENSG00000269190	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1268244	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1268246	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1268253	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs484348	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs494515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs500268	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520340	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541465	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565581	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs579569	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs597561	1.00[ASN][1000 genomes]
rs602031	0.90[AMR][1000 genomes]
rs632308	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs640669	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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

No data

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	chr19:39521400-39523600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:39521400-39523600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:39521400-39523800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:39521600-39522600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
7	chr19:39521600-39522600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
8	chr19:39521600-39522800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:39521600-39522800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
10	chr19:39521600-39522800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
11	chr19:39521600-39522800	Active TSS	NHDF-Ad	bronchial
12	chr19:39521600-39523000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:39521600-39523200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:39521600-39523200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:39521600-39523400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:39521600-39523600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr19:39521600-39523600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:39521600-39523600	Active TSS	Rectal Smooth Muscle	rectum
19	chr19:39521600-39523800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:39521600-39523800	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr19:39521800-39522600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
22	chr19:39521800-39522600	Active TSS	Fetal Kidney	kidney
23	chr19:39521800-39522800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:39521800-39522800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:39521800-39522800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:39521800-39522800	Flanking Active TSS	Right Ventricle	heart
27	chr19:39521800-39522800	Active TSS	A549	lung
28	chr19:39521800-39522800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr19:39521800-39523000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:39521800-39523000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:39521800-39523000	Active TSS	Pancreas	Pancrea
32	chr19:39521800-39523200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:39521800-39523200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr19:39521800-39523200	Active TSS	Fetal Intestine Large	intestine
35	chr19:39521800-39523200	Transcr. at gene 5' and 3'	Right Atrium	heart
36	chr19:39521800-39523200	Active TSS	HSMM	muscle
37	chr19:39521800-39523400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39521800-39523400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr19:39521800-39523400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:39521800-39523400	Active TSS	Brain Substantia Nigra	brain
41	chr19:39521800-39523400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr19:39521800-39523400	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr19:39521800-39523400	Active TSS	HepG2	liver
44	chr19:39521800-39523600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr19:39521800-39523600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:39521800-39523600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
47	chr19:39521800-39523800	Active TSS	Brain Anterior Caudate	brain
48	chr19:39521800-39523800	Active TSS	Brain Hippocampus Middle	brain
49	chr19:39522000-39522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr19:39522000-39522600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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