Variant report

Variant	rs565512501
Chromosome Location	chr4:102268966-102268967
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	MYC	chr4:102268839-102269285	MCF-7	breast:	n/a	chr4:102269253-102269263
2	POLR2A	chr4:102267755-102269525	SK-N-MC	brain:	n/a	n/a
3	RFX5	chr4:102268839-102269039	HepG2	liver:	n/a	n/a
4	REST	chr4:102268771-102269408	A549	lung:	n/a	chr4:102268975-102268988 chr4:102269341-102269350 chr4:102269341-102269354
5	TAF1	chr4:102268813-102269550	H1-neurons	neurons:	n/a	n/a
6	HEY1	chr4:102268804-102269159	HepG2	liver:	n/a	n/a
7	MYC	chr4:102268203-102269513	K562	blood:	n/a	chr4:102269253-102269263 chr4:102268341-102268350 chr4:102268753-102268763
8	TAF1	chr4:102268226-102269558	HepG2	liver:	n/a	n/a
9	MAX	chr4:102267621-102270023	A549	lung:	n/a	chr4:102269253-102269263 chr4:102267703-102267712 chr4:102268341-102268350 chr4:102268753-102268763 chr4:102269560-102269569
10	MAZ	chr4:102266360-102270194	IMR90	lung:	n/a	chr4:102269253-102269263 chr4:102267703-102267712 chr4:102267599-102267609 chr4:102267620-102267630 chr4:102268341-102268350 chr4:102268753-102268763 chr4:102269560-102269569
11	RFX5	chr4:102267228-102271139	SK-N-SH	brain:	n/a	chr4:102270678-102270692 chr4:102270677-102270692 chr4:102270681-102270690
12	MAZ	chr4:102267681-102269587	Hela-S3	cervix:	n/a	chr4:102269253-102269263 chr4:102267703-102267712 chr4:102268341-102268350 chr4:102268753-102268763 chr4:102269560-102269569
13	RAD21	chr4:102267764-102269936	IMR90	lung:	n/a	chr4:102269213-102269222 chr4:102268868-102268878 chr4:102268432-102268446
14	POLR2A	chr4:102268271-102269654	PBDE	blood:	n/a	n/a
15	SP1	chr4:102268525-102270045	HCT-116	colon:	n/a	chr4:102268737-102268751 chr4:102268794-102268806 chr4:102268916-102268925 chr4:102268890-102268904 chr4:102268795-102268804 chr4:102268889-102268900 chr4:102268794-102268806 chr4:102268754-102268768 chr4:102268901-102268912 chr4:102268916-102268925 chr4:102268917-102268926 chr4:102269941-102269955 chr4:102268915-102268927 chr4:102268915-102268926 chr4:102269249-102269263 chr4:102268778-102268792 chr4:102268828-102268849 chr4:102268796-102268805
16	TCF12	chr4:102267722-102269694	ECC-1	luminal epithelium:	n/a	chr4:102268440-102268447
17	USF1	chr4:102268686-102269081	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr4:102268355-102269789	A549	lung:	n/a	n/a
19	POLR2A	chr4:102268894-102269309	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr4:102266321-102270331	IMR90	lung:	n/a	n/a
21	MYC	chr4:102267711-102269803	MCF10A-Er-Src	breast:	n/a	chr4:102269253-102269263 chr4:102268341-102268350 chr4:102268753-102268763 chr4:102269560-102269569
22	POLR2A	chr4:102266637-102269622	GM19193	blood:	n/a	n/a
23	SP1	chr4:102268527-102269682	A549	lung:	n/a	chr4:102268737-102268751 chr4:102268794-102268806 chr4:102268916-102268925 chr4:102268890-102268904 chr4:102268795-102268804 chr4:102268889-102268900 chr4:102268794-102268806 chr4:102268754-102268768 chr4:102268901-102268912 chr4:102268916-102268925 chr4:102268917-102268926 chr4:102268915-102268927 chr4:102268915-102268926 chr4:102269249-102269263 chr4:102268778-102268792 chr4:102268828-102268849 chr4:102268796-102268805
24	SIN3AK20	chr4:102267735-102269786	MCF-7	breast:	n/a	n/a
25	POLR2A	chr4:102268619-102269551	U87	brain:	n/a	n/a
26	EBF1	chr4:102268751-102269148	GM12878	blood:	n/a	n/a
27	SP2	chr4:102268704-102269019	H1-hESC	embryonic stem cell:	n/a	chr4:102268837-102268847 chr4:102268841-102268864 chr4:102268808-102268823 chr4:102268918-102268927
28	TBL1XR1	chr4:102268945-102269542	GM12878	blood:	n/a	n/a
29	PBX3	chr4:102268721-102268997	GM12878	blood:	n/a	chr4:102268838-102268847 chr4:102268842-102268862
30	RAD21	chr4:102268792-102269708	SK-N-SH_RA	brain:	n/a	chr4:102269213-102269222 chr4:102268868-102268878
31	UBTF	chr4:102267795-102269727	K562	blood:	n/a	n/a
32	SIN3AK20	chr4:102268789-102269595	PFSK-1	brain:	n/a	n/a
33	USF1	chr4:102268646-102269041	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr4:102268422-102269869	SK-N-SH_RA	brain:	n/a	chr4:102269213-102269222 chr4:102268868-102268878 chr4:102268432-102268446
35	CEBPD	chr4:102268454-102269260	HepG2	liver:	n/a	n/a
36	TBL1XR1	chr4:102268934-102269076	K562	blood:	n/a	n/a
37	POLR2A	chr4:102268597-102269714	U87	brain:	n/a	n/a
38	E2F4	chr4:102268641-102269575	MCF10A-Er-Src	breast:	n/a	chr4:102268807-102268819 chr4:102268796-102268805
39	TAF1	chr4:102268853-102269190	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr4:102268544-102269410	SK-N-SH_RA	brain:	n/a	chr4:102269310-102269319 chr4:102268751-102268760
41	E2F6	chr4:102268789-102269402	A549	lung:	n/a	chr4:102268807-102268819 chr4:102268796-102268805
42	RFX5	chr4:102268276-102269616	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr4:102268851-102269171	HepG2	liver:	n/a	n/a
44	MYC	chr4:102268924-102269011	HUVEC	blood vessel:	n/a	n/a
45	TBP	chr4:102268826-102269405	HepG2	liver:	n/a	n/a
46	SIN3AK20	chr4:102268773-102269491	H1-hESC	embryonic stem cell:	n/a	n/a
47	NFYB	chr4:102268601-102269044	GM12878	blood:	n/a	chr4:102268836-102268850 chr4:102268837-102268852 chr4:102268839-102268851
48	RCOR1	chr4:102268905-102269453	GM12878	blood:	n/a	n/a
49	CTCF	chr4:102268940-102269090	HRE	kidney:	n/a	n/a
50	POLR2A	chr4:102268849-102269221	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:102268949-102268999	BJ	skin:	n/a
2	chr4:102268949-102268999	HUVEC	blood vessel:	n/a
3	chr4:102268957-102269007	HIPEpiC	eye:	n/a
4	chr4:102268957-102269007	ECC-1	luminal epithelium:	n/a
5	chr4:102268949-102268999	U87	brain:	n/a
6	chr4:102268949-102268999	NB4	blood:	n/a
7	chr4:102268957-102269007	PFSK-1	brain:	n/a
8	chr4:102268957-102269007	AG04450	lung:	fetal
9	chr4:102268957-102269007	SK-N-SH	brain:	n/a
10	chr4:102268949-102268999	H1-hESC	embryonic stem cell:	embryo
11	chr4:102268949-102268999	GM06990	blood:	n/a
12	chr4:102268957-102269007	PrEC	prostate:	n/a
13	chr4:102268949-102268999	HepG2	liver:	n/a
14	chr4:102268957-102269007	MCF10A-Er-Src	breast:	n/a
15	chr4:102268949-102268999	Hepatocyte	liver:	n/a
16	chr4:102268949-102268999	SAEC	small airway:	n/a
17	chr4:102268957-102269007	BJ	skin:	n/a
18	chr4:102268957-102269007	HCT-116	colon:	n/a
19	chr4:102268957-102269007	NHDF-neo	bronchial:	n/a
20	chr4:102268957-102269007	HEEpiC	esophagus:	n/a
21	chr4:102268949-102268999	HCT-116	colon:	n/a
22	chr4:102268949-102268999	T-47D	breast:	n/a
23	chr4:102268957-102269007	ProgFib	skin:	n/a
24	chr4:102268957-102269007	CMK	blood:	n/a
25	chr4:102268949-102268999	GM12891	blood:	n/a
26	chr4:102268957-102269007	HUVEC	blood vessel:	n/a
27	chr4:102268949-102268999	HCPEpiC	choroid plexus:	n/a
28	chr4:102268957-102269007	HRCEpiC	kidney:	n/a
29	chr4:102268949-102268999	HAEpiC	amniotic membrane:	n/a
30	chr4:102268957-102269007	H1-hESC	embryonic stem cell:	embryo
31	chr4:102268949-102268999	NHBE	bronchial:	n/a
32	chr4:102268957-102269007	SKMC	muscle:	n/a
33	chr4:102268957-102269007	SK-N-MC	brain:	n/a
34	chr4:102268949-102268999	GM19239	blood:	n/a
35	chr4:102268949-102268999	LNCaP	prostate:	n/a
36	chr4:102268957-102269007	IMR90	lung:	fetal
37	chr4:102268949-102268999	HRE	kidney:	n/a
38	chr4:102268949-102268999	ovcar-3	ovarian:	n/a
39	chr4:102268949-102268999	AG04450	lung:	fetal
40	chr4:102268957-102269007	AG10803	skin:	n/a
41	chr4:102268949-102268999	SKMC	muscle:	n/a
42	chr4:102268949-102268999	HRCEpiC	kidney:	n/a
43	chr4:102268957-102269007	Hela-S3	cervix:	n/a
44	chr4:102268957-102269007	HMEC	breast:	n/a
45	chr4:102268949-102268999	GM12878	blood:	n/a
46	chr4:102268957-102269007	GM12878	blood:	n/a
47	chr4:102268957-102269007	RPTEC	kidney:	n/a
48	chr4:102268957-102269007	HL-60	blood:	n/a
49	chr4:102268949-102268999	SK-N-SH_RA	brain:	n/a
50	chr4:102268957-102269007	GM19239	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100869383..100871934-chr4:102267599..102271042,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP001816.1.1-1	chr4:102268934-102269166	NR_033874

Variant related genes	Relation type
PPP3CA	TF binding region
PPP3CA	CpG island
ENSG00000245322	Chromatin interaction
ENSG00000164032	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	esv3374573	chr4:102266354-102269502	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3413525	chr4:102266529-102269802	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3408421	chr4:102267454-102270302	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr4:102265600-102269800	Active TSS	NHLF	lung
2	chr4:102265800-102269800	Active TSS	Brain Angular Gyrus	brain
3	chr4:102265800-102270000	Active TSS	Fetal Kidney	kidney
4	chr4:102266000-102269000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:102266200-102269800	Active TSS	Right Atrium	heart
6	chr4:102266200-102270000	Active TSS	Aorta	Aorta
7	chr4:102266200-102270000	Active TSS	Ovary	ovary
8	chr4:102266400-102269600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:102266400-102269600	Active TSS	Fetal Stomach	stomach
10	chr4:102266400-102269600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr4:102266400-102269800	Active TSS	Brain Hippocampus Middle	brain
12	chr4:102266400-102269800	Active TSS	Small Intestine	intestine
13	chr4:102266400-102269800	Active TSS	HSMM	muscle
14	chr4:102266400-102270000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:102266400-102270000	Active TSS	Brain Cingulate Gyrus	brain
16	chr4:102266400-102270000	Active TSS	Gastric	stomach
17	chr4:102266400-102270200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:102266600-102269000	Active TSS	Fetal Muscle Trunk	muscle
19	chr4:102266600-102269600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr4:102266600-102269600	Active TSS	Colonic Mucosa	Colon
21	chr4:102266600-102269800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:102266600-102269800	Active TSS	Colon Smooth Muscle	Colon
23	chr4:102266600-102269800	Active TSS	Lung	lung
24	chr4:102266600-102270000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:102266600-102270000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr4:102266600-102270200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr4:102266600-102270200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:102266600-102270200	Active TSS	A549	lung
29	chr4:102266600-102270400	Active TSS	Rectal Smooth Muscle	rectum
30	chr4:102266800-102269200	Active TSS	HepG2	liver
31	chr4:102266800-102269600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:102266800-102269600	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr4:102266800-102269800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:102266800-102269800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr4:102266800-102269800	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr4:102266800-102269800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:102266800-102269800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:102266800-102269800	Active TSS	Brain Substantia Nigra	brain
39	chr4:102266800-102269800	Active TSS	Right Ventricle	heart
40	chr4:102266800-102269800	Active TSS	NHEK	skin
41	chr4:102266800-102270000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:102266800-102270000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:102266800-102270000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr4:102266800-102270000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:102266800-102270000	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr4:102266800-102270000	Active TSS	Brain Anterior Caudate	brain
47	chr4:102266800-102270000	Active TSS	Fetal Brain Female	brain
48	chr4:102266800-102270200	Active TSS	H1 Cell Line	embryonic stem cell
49	chr4:102266800-102270200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:102266800-102270200	Active TSS	HSMMtube	muscle

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