Variant report

Variant	rs640669
Chromosome Location	chr19:39523341-39523342
allele	A/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	POLR2A	chr19:39523237-39523454	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:39523002-39523583	K562	blood:	n/a	n/a
3	E2F6	chr19:39523060-39523528	H1-hESC	embryonic stem cell:	n/a	chr19:39523144-39523154
4	E2F6	chr19:39523034-39523664	H1-hESC	embryonic stem cell:	n/a	chr19:39523144-39523154
5	RCOR1	chr19:39523105-39523452	K562	blood:	n/a	n/a
6	CHD2	chr19:39523048-39523523	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr19:39523129-39523467	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr19:39523007-39523567	H1-hESC	embryonic stem cell:	n/a	chr19:39523280-39523291 chr19:39523221-39523232 chr19:39523106-39523117
9	POLR2A	chr19:39521624-39523805	K562	blood:	n/a	n/a
10	TCF7L2	chr19:39523156-39523865	PANC-1	pancreas:	n/a	n/a
11	E2F6	chr19:39523195-39523432	K562	blood:	n/a	n/a
12	TCF12	chr19:39523071-39523562	H1-hESC	embryonic stem cell:	n/a	n/a
13	CBX3	chr19:39523245-39523577	K562	blood:	n/a	n/a
14	MAX	chr19:39523187-39523445	K562	blood:	n/a	n/a
15	UBTF	chr19:39523271-39523678	K562	blood:	n/a	n/a
16	NR2F2	chr19:39523263-39523827	K562	blood:	n/a	n/a
17	SP4	chr19:39523013-39523472	H1-hESC	embryonic stem cell:	n/a	n/a
18	SIN3AK20	chr19:39521478-39523896	PANC-1	pancreas:	n/a	n/a
19	MAX	chr19:39522835-39523565	H1-hESC	embryonic stem cell:	n/a	chr19:39522871-39522881
20	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
21	SIN3AK20	chr19:39521601-39523985	PANC-1	pancreas:	n/a	n/a
22	SP1	chr19:39523029-39523640	H1-hESC	embryonic stem cell:	n/a	chr19:39523196-39523206 chr19:39523227-39523239 chr19:39523229-39523238 chr19:39523289-39523302 chr19:39523228-39523237 chr19:39523227-39523239
23	MYC	chr19:39523158-39523358	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:39520454-39524689	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr19:39521695-39523527	MCF-7	breast:	n/a	n/a
26	TCF12	chr19:39521363-39523919	A549	lung:	n/a	n/a
27	CREB1	chr19:39522872-39523526	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUND	chr19:39523257-39523411	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr19:39523336-39523504	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBP	chr19:39523232-39523455	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr19:39521380-39523937	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
32	POLR2A	chr19:39521711-39523436	A549	lung:	n/a	n/a
33	POLR2A	chr19:39521784-39523389	MCF-7	breast:	n/a	n/a
34	POLR2A	chr19:39523063-39523396	A549	lung:	n/a	n/a
35	POLR2A	chr19:39522837-39523509	H1-hESC	embryonic stem cell:	n/a	n/a
36	YY1	chr19:39523275-39523577	GM12878	blood:	n/a	chr19:39523280-39523291
37	CCNT2	chr19:39521775-39523522	K562	blood:	n/a	chr19:39523229-39523238 chr19:39522088-39522097 chr19:39522023-39522032
38	POLR2A	chr19:39522991-39523517	HCT-116	colon:	n/a	n/a
39	MAZ	chr19:39523140-39523462	GM12878	blood:	n/a	n/a
40	YY1	chr19:39523228-39523531	K562	blood:	n/a	chr19:39523280-39523291
41	REST	chr19:39521568-39523982	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr19:39522990-39523465	K562	blood:	n/a	n/a
43	POLR2A	chr19:39521660-39523415	MCF-7	breast:	n/a	n/a
44	E2F6	chr19:39521584-39523594	A549	lung:	n/a	chr19:39522088-39522097 chr19:39523144-39523154
45	RAD21	chr19:39523277-39523457	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:39519979-39524546	PANC-1	pancreas:	n/a	n/a
47	TAF1	chr19:39523067-39523470	H1-hESC	embryonic stem cell:	n/a	n/a
48	CREB1	chr19:39521653-39523471	A549	lung:	n/a	n/a
49	POLR2A	chr19:39523253-39523391	A549	lung:	n/a	n/a
50	SIN3A	chr19:39521612-39523514	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39523309-39523359	Jurkat	blood:	n/a
2	chr19:39523339-39523389	PANC-1	pancreas:	n/a
3	chr19:39523309-39523359	HIPEpiC	eye:	n/a
4	chr19:39523309-39523359	GM06990	blood:	n/a
5	chr19:39523309-39523359	GM12892	blood:	n/a
6	chr19:39523339-39523389	SKMC	muscle:	n/a
7	chr19:39523309-39523359	HNPCEpiC	eye:	n/a
8	chr19:39523309-39523359	GM12878	blood:	n/a
9	chr19:39523309-39523359	HRCEpiC	kidney:	n/a
10	chr19:39523339-39523389	PrEC	prostate:	n/a
11	chr19:39523339-39523389	NHDF-neo	bronchial:	n/a
12	chr19:39523339-39523389	NT2-D1	testis:	n/a
13	chr19:39523339-39523389	HEK293	kidney:	embryo
14	chr19:39523309-39523359	HCM	heart:	n/a
15	chr19:39523339-39523389	AG09319	gingival:	n/a
16	chr19:39523309-39523359	CMK	blood:	n/a
17	chr19:39523339-39523389	Hepatocyte	liver:	n/a
18	chr19:39523309-39523359	SK-N-MC	brain:	n/a
19	chr19:39523309-39523359	ECC-1	luminal epithelium:	n/a
20	chr19:39523339-39523389	HRCEpiC	kidney:	n/a
21	chr19:39523339-39523389	NHBE	bronchial:	n/a
22	chr19:39523309-39523359	HAEpiC	amniotic membrane:	n/a
23	chr19:39523339-39523389	IMR90	lung:	fetal
24	chr19:39523339-39523389	AoSMC	blood vessel:	n/a
25	chr19:39523339-39523389	GM12878	blood:	n/a
26	chr19:39523339-39523389	HEEpiC	esophagus:	n/a
27	chr19:39523339-39523389	HCT-116	colon:	n/a
28	chr19:39523309-39523359	HEEpiC	esophagus:	n/a
29	chr19:39523309-39523359	NHDF-neo	bronchial:	n/a
30	chr19:39523309-39523359	HCPEpiC	choroid plexus:	n/a
31	chr19:39523339-39523389	NB4	blood:	n/a
32	chr19:39523309-39523359	T-47D	breast:	n/a
33	chr19:39523309-39523359	AG04450	lung:	fetal
34	chr19:39523309-39523359	SKMC	muscle:	n/a
35	chr19:39523339-39523389	AG09309	skin:	n/a
36	chr19:39523309-39523359	NB4	blood:	n/a
37	chr19:39523339-39523389	PFSK-1	brain:	n/a
38	chr19:39523309-39523359	GM12891	blood:	n/a
39	chr19:39523339-39523389	HPAEpiC	pulmonary alveolar:	n/a
40	chr19:39523309-39523359	HRE	kidney:	n/a
41	chr19:39523309-39523359	NT2-D1	testis:	n/a
42	chr19:39523309-39523359	SK-N-SH_RA	brain:	n/a
43	chr19:39523339-39523389	AG04450	lung:	fetal
44	chr19:39523309-39523359	AG09309	skin:	n/a
45	chr19:39523309-39523359	PFSK-1	brain:	n/a
46	chr19:39523339-39523389	BJ	skin:	n/a
47	chr19:39523309-39523359	AG09319	gingival:	n/a
48	chr19:39523309-39523359	NH-A	brain:	n/a
49	chr19:39523339-39523389	HUVEC	blood vessel:	n/a
50	chr19:39523339-39523389	HNPCEpiC	eye:	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
ENSG00000130669	Chromatin interaction
ENSG00000269190	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	1.00[ASN][1000 genomes]
rs1268246	1.00[ASN][1000 genomes]
rs1268253	1.00[ASN][1000 genomes]
rs484348	1.00[ASN][1000 genomes]
rs494515	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs500268	1.00[ASN][1000 genomes]
rs520340	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541465	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565581	1.00[ASN][1000 genomes]
rs579569	1.00[ASN][1000 genomes]
rs597561	1.00[ASN][1000 genomes]
rs632308	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636534	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674440	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8111459	1.00[JPT][hapmap]

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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39521000-39523600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:39521400-39523600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:39521400-39523600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:39521400-39523800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:39521600-39523400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr19:39521600-39523600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:39521600-39523600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:39521600-39523600	Active TSS	Rectal Smooth Muscle	rectum
9	chr19:39521600-39523800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:39521600-39523800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr19:39521800-39523400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:39521800-39523400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:39521800-39523400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:39521800-39523400	Active TSS	Brain Substantia Nigra	brain
15	chr19:39521800-39523400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr19:39521800-39523400	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr19:39521800-39523400	Active TSS	HepG2	liver
18	chr19:39521800-39523600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr19:39521800-39523600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:39521800-39523600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr19:39521800-39523800	Active TSS	Brain Anterior Caudate	brain
22	chr19:39521800-39523800	Active TSS	Brain Hippocampus Middle	brain
23	chr19:39522000-39523400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr19:39522000-39523400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr19:39522000-39523400	Active TSS	Aorta	Aorta
26	chr19:39522000-39523400	Active TSS	Brain Cingulate Gyrus	brain
27	chr19:39522000-39523400	Active TSS	Left Ventricle	heart
28	chr19:39522000-39523400	Active TSS	Ovary	ovary
29	chr19:39522000-39523600	Active TSS	Brain Angular Gyrus	brain
30	chr19:39522000-39523600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr19:39522000-39523600	Active TSS	Colon Smooth Muscle	Colon
32	chr19:39522000-39523600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr19:39522000-39523800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:39522000-39523800	Enhancers	Fetal Heart	heart
35	chr19:39522200-39523400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:39522200-39523400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
37	chr19:39522200-39523400	Flanking Active TSS	HMEC	breast
38	chr19:39522200-39523400	Active TSS	Osteobl	bone
39	chr19:39522200-39523600	Active TSS	Gastric	stomach
40	chr19:39522400-39523400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:39522400-39523600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:39522400-39523600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr19:39522600-39523400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:39522600-39523400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:39522600-39523400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:39522600-39523400	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr19:39522600-39523400	Flanking Active TSS	NHEK	skin
48	chr19:39522600-39523600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr19:39522600-39523600	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr19:39522800-39523400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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