Variant report

Variant	rs569019990
Chromosome Location	chr3:23986274-23986275
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	MAX	chr3:23986061-23988244	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
2	MAX	chr3:23986260-23988309	HCT-116	colon:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
3	MYC	chr3:23985630-23988292	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23985779-23985795 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
4	POLR2A	chr3:23986205-23988171	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:23986095-23988262	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr3:23986104-23988409	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr3:23986220-23988203	HepG2	liver:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
8	E2F6	chr3:23986183-23986754	A549	lung:	n/a	chr3:23986483-23986490 chr3:23986479-23986491 chr3:23986483-23986490 chr3:23986483-23986490
9	MAZ	chr3:23985991-23988385	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
10	POLR2A	chr3:23986132-23988235	K562	blood:	n/a	n/a
11	REST	chr3:23985970-23988483	H1-neurons	neurons:	n/a	chr3:23988106-23988119 chr3:23986726-23986739 chr3:23988103-23988116
12	ZBTB7A	chr3:23986178-23986704	ECC-1	luminal epithelium:	n/a	n/a
13	TBP	chr3:23986094-23988447	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr3:23986016-23989986	IMR90	lung:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
15	CEBPB	chr3:23986234-23986523	HepG2	liver:	n/a	n/a
16	MYC	chr3:23985627-23988307	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23985779-23985795 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
17	ZBTB7A	chr3:23986228-23987996	K562	blood:	n/a	chr3:23987122-23987131 chr3:23986953-23986961 chr3:23987571-23987578 chr3:23986962-23986973 chr3:23986961-23986972
18	POLR2A	chr3:23985541-23990663	H1-hESC	embryonic stem cell:	n/a	n/a
19	MXI1	chr3:23985307-23988519	SK-N-SH	brain:	n/a	chr3:23987345-23987354
20	CHD2	chr3:23986130-23986942	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:23986254-23986877	SK-N-MC	brain:	n/a	n/a
22	HCFC1	chr3:23985923-23988484	Hela-S3	cervix:	n/a	n/a
23	JUND	chr3:23986133-23986903	H1-hESC	embryonic stem cell:	n/a	chr3:23986448-23986457
24	TAF1	chr3:23986178-23988204	H1-hESC	embryonic stem cell:	n/a	n/a
25	RCOR1	chr3:23985950-23986922	K562	blood:	n/a	n/a
26	REST	chr3:23986215-23986767	H1-neurons	neurons:	n/a	chr3:23986726-23986739
27	POLR2A	chr3:23986258-23988270	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr3:23986252-23986990	MCF-7	breast:	n/a	chr3:23986729-23986739
29	MAX	chr3:23986188-23988424	A549	lung:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
30	CHD2	chr3:23986109-23986838	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:23986213-23988189	H1-neurons	neurons:	n/a	n/a
32	BHLHE40	chr3:23985728-23988393	K562	blood:	n/a	chr3:23986706-23986722 chr3:23986783-23986799 chr3:23987153-23987169 chr3:23987430-23987446 chr3:23987438-23987454 chr3:23987441-23987457 chr3:23987189-23987205
33	SIN3AK20	chr3:23986223-23988484	MCF-7	breast:	n/a	n/a
34	RCOR1	chr3:23985939-23986993	K562	blood:	n/a	n/a
35	MXI1	chr3:23985536-23988397	IMR90	lung:	n/a	chr3:23987345-23987354
36	TBP	chr3:23986109-23988318	K562	blood:	n/a	n/a
37	SIN3A	chr3:23985912-23988449	H1-hESC	embryonic stem cell:	n/a	chr3:23987199-23987210 chr3:23987852-23987863 chr3:23986774-23986785 chr3:23986898-23986909
38	TAF1	chr3:23986236-23988256	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr3:23986245-23988392	HCT-116	colon:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
40	NR3C1	chr3:23986248-23987054	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78422464..78425441-chr3:23985742..23987944,2	MCF-7	breast:
2	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
3	chr3:23986158..23988420-chr3:24004373..24006448,3	MCF-7	breast:
4	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
5	chr3:23985869..23987641-chr3:24536460..24539004,2	MCF-7	breast:
6	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region
ENSG00000228791	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000166411	Chromatin interaction
ENSG00000136425	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3449153	chr3:23984948-23988646	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3406325	chr3:23985473-23988321	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3425301	chr3:23985548-23988496	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23985400-23986600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:23985600-23986400	Bivalent/Poised TSS	Thymus	Thymus
3	chr3:23985600-23986600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:23985600-23988200	Active TSS	Fetal Kidney	kidney
5	chr3:23985600-23988400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:23985600-23988800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:23985800-23986600	Active TSS	Primary T cells from cord blood	blood
8	chr3:23985800-23987600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:23985800-23987800	Active TSS	Colonic Mucosa	Colon
10	chr3:23985800-23988000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr3:23985800-23988000	Active TSS	Brain Substantia Nigra	brain
12	chr3:23985800-23988200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:23985800-23988200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:23985800-23988200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:23985800-23988200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:23985800-23988200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:23985800-23988200	Active TSS	Lung	lung
18	chr3:23985800-23988400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:23985800-23988400	Active TSS	Fetal Brain Female	brain
20	chr3:23985800-23988400	Active TSS	Psoas Muscle	Psoas
21	chr3:23985800-23988600	Active TSS	Brain Anterior Caudate	brain
22	chr3:23985800-23988800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:23986000-23986400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr3:23986000-23986400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
25	chr3:23986000-23986400	Active TSS	Right Atrium	heart
26	chr3:23986000-23986600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:23986000-23986600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
28	chr3:23986000-23986600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr3:23986000-23986600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:23986000-23986600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
31	chr3:23986000-23986600	Flanking Bivalent TSS/Enh	Dnd41	blood
32	chr3:23986000-23987800	Active TSS	Fetal Muscle Trunk	muscle
33	chr3:23986000-23988000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:23986000-23988000	Active TSS	Left Ventricle	heart
35	chr3:23986000-23988000	Active TSS	NHEK	skin
36	chr3:23986000-23988200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr3:23986000-23988200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr3:23986000-23988200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr3:23986000-23988200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:23986000-23988200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:23986000-23988200	Active TSS	Colon Smooth Muscle	Colon
42	chr3:23986000-23988200	Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:23986000-23988400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:23986000-23988400	Active TSS	Right Ventricle	heart
45	chr3:23986000-23988600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:23986000-23988600	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:23986000-23988600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:23986000-23988800	Active TSS	Aorta	Aorta
49	chr3:23986000-23988800	Active TSS	Ovary	ovary
50	chr3:23986200-23986400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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