Variant report

Variant	rs539579958
Chromosome Location	chr1:173445645-173445646
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	PML	chr1:173445618-173446355	K562	blood:	n/a	n/a
2	REST	chr1:173445635-173447170	H1-neurons	neurons:	n/a	chr1:173446675-173446688
3	TRIM28	chr1:173445323-173446776	K562	blood:	n/a	n/a
4	CHD1	chr1:173445589-173446258	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:173445243-173447743	Hela-S3	cervix:	n/a	n/a
6	MAX	chr1:173445619-173447723	HCT-116	colon:	n/a	n/a
7	FOS	chr1:173444797-173445874	MCF10A-Er-Src	breast:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
8	POLR2A	chr1:173445641-173446914	PFSK-1	brain:	n/a	n/a
9	SIN3AK20	chr1:173445582-173447941	MCF-7	breast:	n/a	n/a
10	GATA3	chr1:173445489-173445753	SH-SY5Y	brain:	n/a	n/a
11	CEBPB	chr1:173445631-173446009	K562	blood:	n/a	n/a
12	RUNX3	chr1:173445497-173446361	GM12878	blood:	n/a	n/a
13	ZKSCAN1	chr1:173444907-173447574	Hela-S3	cervix:	n/a	n/a
14	ZNF143	chr1:173445426-173446204	K562	blood:	n/a	n/a
15	STAT3	chr1:173445629-173445954	MCF10A-Er-Src	breast:	n/a	chr1:173445728-173445740
16	CBX3	chr1:173444903-173446307	K562	blood:	n/a	chr1:173444947-173444958
17	TEAD4	chr1:173445087-173446288	K562	blood:	n/a	n/a
18	MXI1	chr1:173444253-173448100	IMR90	lung:	n/a	chr1:173447831-173447846
19	BHLHE40	chr1:173444953-173447722	K562	blood:	n/a	chr1:173446795-173446811
20	NR2F2	chr1:173445330-173446336	K562	blood:	n/a	n/a
21	CEBPB	chr1:173445639-173447787	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr1:173445625-173446086	MCF-7	breast:	n/a	n/a
23	MAX	chr1:173445044-173447710	Hela-S3	cervix:	n/a	n/a
24	STAT3	chr1:173445640-173445954	MCF10A-Er-Src	breast:	n/a	chr1:173445728-173445740
25	USF2	chr1:173444976-173446389	Hela-S3	cervix:	n/a	n/a
26	KAP1	chr1:173444758-173446206	HEK293	kidney:	n/a	n/a
27	MYC	chr1:173445607-173445953	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr1:173445606-173446319	GM12878	blood:	n/a	n/a
29	SMC3	chr1:173444910-173448008	Hela-S3	cervix:	n/a	n/a
30	NFIC	chr1:173445618-173446294	GM12878	blood:	n/a	n/a
31	FOS	chr1:173445630-173446337	MCF10A-Er-Src	breast:	n/a	n/a
32	BRCA1	chr1:173445575-173446689	Hela-S3	cervix:	n/a	n/a
33	STAT3	chr1:173445624-173445963	MCF10A-Er-Src	breast:	n/a	chr1:173445728-173445740
34	MYC	chr1:173445606-173445782	MCF10A-Er-Src	breast:	n/a	n/a
35	USF2	chr1:173445479-173445662	K562	blood:	n/a	n/a
36	SIN3A	chr1:173445410-173447767	H1-hESC	embryonic stem cell:	n/a	chr1:173447160-173447168 chr1:173447668-173447676 chr1:173446722-173446733
37	EGR1	chr1:173445436-173445694	K562	blood:	n/a	chr1:173445601-173445614
38	USF1	chr1:173445153-173446616	K562	blood:	n/a	chr1:173446173-173446184
39	JUN	chr1:173444105-173448462	K562	blood:	n/a	chr1:173446953-173446961 chr1:173445057-173445067 chr1:173447039-173447048 chr1:173445057-173445067
40	EP300	chr1:173444878-173445682	K562	blood:	n/a	chr1:173445337-173445353
41	POLR2A	chr1:173445601-173446324	HUVEC	blood vessel:	n/a	n/a
42	HCFC1	chr1:173444740-173448059	Hela-S3	cervix:	n/a	n/a
43	SPI1	chr1:173445595-173446314	HL-60	blood:	n/a	n/a
44	GTF2F1	chr1:173444906-173447824	Hela-S3	cervix:	n/a	n/a
45	MTA3	chr1:173445401-173446289	GM12878	blood:	n/a	n/a
46	MXI1	chr1:173444135-173448173	SK-N-SH	brain:	n/a	chr1:173447831-173447846
47	MAZ	chr1:173444567-173447830	IMR90	lung:	n/a	n/a
48	USF1	chr1:173445630-173447722	HCT-116	colon:	n/a	chr1:173446173-173446184 chr1:173446795-173446811
49	MXI1	chr1:173445630-173448026	Hela-S3	cervix:	n/a	chr1:173447831-173447846
50	PML	chr1:173445529-173446981	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173444743..173447866-chr1:173792301..173795321,5	MCF-7	breast:
2	chr1:173442552..173449186-chr1:173835087..173838637,8	MCF-7	breast:
3	chr1:173444678..173448018-chr1:173835571..173838629,5	K562	blood:
4	chr1:173445302..173447387-chr1:173760235..173762454,2	MCF-7	breast:
5	chr1:173442536..173447801-chr1:173833439..173838851,7	K562	blood:
6	chr1:173444899..173448691-chr1:173990820..173993753,4	MCF-7	breast:
7	chr1:173445270..173447365-chr22:21995394..21997975,2	K562	blood:
8	chr1:173443316..173450639-chr1:173791413..173797919,15	K562	blood:
9	chr1:173445598..173446579-chr1:173683742..173684289,2	Hela-S3	cervix:
10	chr1:173443428..173450639-chr1:173791407..173797248,10	K562	blood:
11	chr1:173445295..173447440-chr17:58469252..58471783,2	MCF-7	breast:

Variant related genes	Relation type
PRDX6	TF binding region
ENSG00000141371	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000170832	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000200674	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000128228	Chromatin interaction
ENSG00000208317	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv3356084	chr1:173445354-173448202	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr1:173440600-173445800	Weak transcription	Spleen	Spleen
2	chr1:173443600-173445800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:173443600-173447400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:173443600-173447800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:173443800-173447600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:173444000-173448000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:173444200-173445800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr1:173444200-173445800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:173444200-173446000	Flanking Active TSS	Liver	Liver
10	chr1:173444200-173447400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:173444200-173447400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:173444400-173445800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:173444400-173445800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:173444400-173446200	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr1:173444400-173448600	Active TSS	HSMMtube	muscle
16	chr1:173444600-173445800	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr1:173444600-173445800	Flanking Active TSS	Fetal Heart	heart
18	chr1:173444600-173445800	Flanking Active TSS	Hela-S3	cervix
19	chr1:173444600-173445800	Flanking Active TSS	HMEC	breast
20	chr1:173444600-173445800	Flanking Active TSS	HUVEC	blood vessel
21	chr1:173444600-173447400	Active TSS	Brain Angular Gyrus	brain
22	chr1:173444800-173445800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:173444800-173445800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr1:173444800-173445800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr1:173444800-173445800	Flanking Active TSS	Dnd41	blood
26	chr1:173444800-173449000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:173445000-173445800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr1:173445000-173445800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:173445000-173445800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr1:173445000-173446000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr1:173445000-173446000	Active TSS	Right Atrium	heart
32	chr1:173445000-173447400	Active TSS	Gastric	stomach
33	chr1:173445000-173448200	Active TSS	Fetal Muscle Trunk	muscle
34	chr1:173445200-173445800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:173445200-173445800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:173445200-173445800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:173445200-173445800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr1:173445200-173445800	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr1:173445200-173445800	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr1:173445200-173445800	Flanking Active TSS	Fetal Lung	lung
41	chr1:173445200-173445800	Flanking Active TSS	Stomach Mucosa	stomach
42	chr1:173445200-173446000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:173445200-173446000	Flanking Active TSS	Fetal Thymus	thymus
44	chr1:173445200-173446200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr1:173445200-173446200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:173445200-173446400	Bivalent/Poised TSS	HepG2	liver
47	chr1:173445200-173447000	Active TSS	Fetal Brain Female	brain
48	chr1:173445200-173447400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:173445200-173447600	Active TSS	Aorta	Aorta
50	chr1:173445200-173447600	Active TSS	Small Intestine	intestine

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