Variant report

Variant	rs575929564
Chromosome Location	chr4:144257308-144257309
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	chr4:144257216-144258623	ProgFib	skin:	n/a	n/a
2	HCFC1	chr4:144256838-144257773	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:144256853-144258635	MCF-7	breast:	n/a	n/a
4	MAX	chr4:144257106-144258358	K562	blood:	n/a	chr4:144257518-144257528
5	POLR2A	chr4:144257067-144258383	A549	lung:	n/a	n/a
6	CUX1	chr4:144257287-144257335	GM12878	blood:	n/a	n/a
7	CHD2	chr4:144256922-144258211	GM12878	blood:	n/a	chr4:144257188-144257198 chr4:144257525-144257535
8	MAZ	chr4:144256964-144258564	HepG2	liver:	n/a	chr4:144257518-144257528
9	MAX	chr4:144256886-144257810	A549	lung:	n/a	chr4:144257518-144257528 chr4:144256930-144256940
10	POLR2A	chr4:144256855-144258600	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr4:144256938-144258485	PBDE	blood:	n/a	n/a
12	SIN3A	chr4:144256747-144259474	H1-hESC	embryonic stem cell:	n/a	chr4:144258487-144258500
13	CTCF	chr4:144257300-144257450	HCPEpiC	choroid plexus:	n/a	n/a
14	YY1	chr4:144256822-144257548	GM12878	blood:	n/a	chr4:144257088-144257096 chr4:144257087-144257099 chr4:144257520-144257529 chr4:144257521-144257532
15	ELF1	chr4:144257021-144257492	K562	blood:	n/a	chr4:144257385-144257397
16	ETS1	chr4:144256990-144257581	A549	lung:	n/a	chr4:144257512-144257523 chr4:144257521-144257532 chr4:144257524-144257535 chr4:144257245-144257258 chr4:144257246-144257259 chr4:144257518-144257529
17	SIX5	chr4:144257082-144257453	K562	blood:	n/a	chr4:144257329-144257338
18	CHD2	chr4:144256822-144258175	Hela-S3	cervix:	n/a	chr4:144257188-144257198 chr4:144257525-144257535
19	EP300	chr4:144257005-144257333	GM12878	blood:	n/a	chr4:144257206-144257215
20	RFX5	chr4:144257087-144257374	H1-hESC	embryonic stem cell:	n/a	n/a
21	BHLHE40	chr4:144257181-144258110	GM12878	blood:	n/a	chr4:144257737-144257753
22	YY1	chr4:144256722-144257705	SK-N-SH	brain:	n/a	chr4:144257088-144257096 chr4:144257663-144257677 chr4:144257087-144257099 chr4:144257520-144257529 chr4:144257521-144257532
23	POLR2A	chr4:144257015-144258619	GM18951	blood:	n/a	n/a
24	ZBTB33	chr4:144257153-144257399	A549	lung:	n/a	n/a
25	POLR2A	chr4:144257042-144257835	A549	lung:	n/a	n/a
26	EGR1	chr4:144257158-144257917	K562	blood:	n/a	chr4:144257246-144257270 chr4:144257520-144257530 chr4:144257522-144257536 chr4:144257517-144257527 chr4:144257521-144257534 chr4:144257509-144257522
27	POLR2A	chr4:144257104-144258517	GM19099	blood:	n/a	n/a
28	TBP	chr4:144257119-144257423	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr4:144256860-144258626	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr4:144257018-144257796	SK-N-SH	brain:	n/a	n/a
31	CHD2	chr4:144256870-144257735	HepG2	liver:	n/a	chr4:144257188-144257198 chr4:144257525-144257535
32	TAF1	chr4:144257104-144257770	K562	blood:	n/a	n/a
33	POLR2A	chr4:144257221-144257352	A549	lung:	n/a	n/a
34	YY1	chr4:144256940-144257449	K562	blood:	n/a	chr4:144257088-144257096 chr4:144257087-144257099
35	POLR2A	chr4:144257231-144258464	K562	blood:	n/a	n/a
36	POLR2A	chr4:144257094-144258475	H1-neurons	neurons:	n/a	n/a
37	CBX3	chr4:144256897-144257695	K562	blood:	n/a	n/a
38	MYC	chr4:144257104-144259179	K562	blood:	n/a	chr4:144257518-144257528
39	IRF1	chr4:144257131-144257602	K562	blood:	n/a	n/a
40	E2F4	chr4:144257059-144257732	MCF10A-Er-Src	breast:	n/a	chr4:144257131-144257143 chr4:144257520-144257529
41	TBL1XR1	chr4:144257284-144257769	K562	blood:	n/a	n/a
42	POLR2A	chr4:144257015-144258548	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr4:144256753-144257835	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:144257175-144257567	GM12878	blood:	n/a	n/a
45	HEY1	chr4:144257019-144257773	K562	blood:	n/a	chr4:144257736-144257751
46	MAX	chr4:144256820-144257729	SK-N-SH	brain:	n/a	chr4:144257518-144257528 chr4:144256930-144256940
47	MXI1	chr4:144257066-144257699	H1-hESC	embryonic stem cell:	n/a	n/a
48	CHD2	chr4:144257196-144257643	K562	blood:	n/a	chr4:144257525-144257535
49	GTF2F1	chr4:144256831-144257473	H1-hESC	embryonic stem cell:	n/a	n/a
50	SIX5	chr4:144257025-144257501	H1-hESC	embryonic stem cell:	n/a	chr4:144257329-144257338

No.	Distal block	Cell Line	Cell type
1	chr4:144104958..144107554-chr4:144256815..144258504,3	K562	blood:
2	chr4:124524644..124527323-chr4:144255705..144257566,2	MCF-7	breast:
3	chr4:144104818..144107585-chr4:144256509..144260468,4	MCF-7	breast:
4	chr4:144254658..144259448-chr4:144261105..144264742,6	MCF-7	breast:
5	chr4:144254627..144258395-chr4:144297952..144301828,4	K562	blood:
6	chr4:144256474..144260869-chr4:144433151..144436933,4	K562	blood:
7	chr4:144251943..144253888-chr4:144255920..144257556,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FREM3-6	chr4:144256418-144258970	NONHSAT098553

Variant related genes	Relation type
GAB1	TF binding region
ENSG00000109458	Chromatin interaction
ENSG00000250326	Chromatin interaction
ENSG00000170185	Chromatin interaction
ENSG00000153147	Chromatin interaction
ENSG00000245112	Chromatin interaction
ENSG00000265623	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv3332574	chr4:144239396-144259577	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	esv3406126	chr4:144256927-144259675	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144256000-144259600	Active TSS	Fetal Kidney	kidney
2	chr4:144256200-144259000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:144256600-144257400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr4:144256600-144257400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr4:144256600-144257600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:144256600-144258600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:144256600-144258600	Active TSS	Fetal Muscle Trunk	muscle
8	chr4:144256600-144258800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:144256600-144258800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr4:144256600-144258800	Active TSS	Liver	Liver
11	chr4:144256600-144258800	Active TSS	Hela-S3	cervix
12	chr4:144256600-144259000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:144256600-144259000	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr4:144256600-144259000	Active TSS	HMEC	breast
15	chr4:144256600-144259000	Active TSS	HUVEC	blood vessel
16	chr4:144256600-144259000	Active TSS	NH-A	brain
17	chr4:144256600-144259000	Active TSS	NHEK	skin
18	chr4:144256600-144259000	Active TSS	Osteobl	bone
19	chr4:144256600-144259200	Active TSS	H1 Cell Line	embryonic stem cell
20	chr4:144256600-144259200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:144256600-144259200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:144256600-144259200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:144256600-144259200	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:144256600-144259200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr4:144256600-144259200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:144256600-144259200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:144256600-144259200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:144256600-144259200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:144256600-144259200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:144256600-144259400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr4:144256600-144259400	Active TSS	H9 Cell Line	embryonic stem cell
32	chr4:144256600-144259400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:144256600-144259400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr4:144256600-144259400	Active TSS	Primary T cells from cord blood	blood
35	chr4:144256600-144259400	Active TSS	Fetal Lung	lung
36	chr4:144256600-144259400	Active TSS	A549	lung
37	chr4:144256600-144259400	Active TSS	HSMMtube	muscle
38	chr4:144256600-144259600	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr4:144256600-144259600	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr4:144256600-144259600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:144256600-144259600	Active TSS	Psoas Muscle	Psoas
42	chr4:144256600-144259600	Active TSS	Rectal Smooth Muscle	rectum
43	chr4:144256600-144259600	Active TSS	Stomach Smooth Muscle	stomach
44	chr4:144256600-144259800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:144256600-144259800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:144256600-144259800	Active TSS	Colon Smooth Muscle	Colon
47	chr4:144256600-144259800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr4:144256600-144259800	Active TSS	Fetal Intestine Large	intestine
49	chr4:144256600-144259800	Active TSS	Ovary	ovary
50	chr4:144256600-144259800	Active TSS	Rectal Mucosa Donor 31	rectum

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