Variant report

Variant	rs12749440
Chromosome Location	chr1:166808809-166808810
allele	A/C
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	CTCF	chr1:166808610-166808832	MCF-7	breast:	n/a	n/a
2	MAX	chr1:166808252-166808891	HUVEC	blood vessel:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166808709-166808718
3	POLR2A	chr1:166808034-166809618	GM12892	blood:	n/a	n/a
4	EGR1	chr1:166808310-166808940	H1-hESC	embryonic stem cell:	n/a	chr1:166808416-166808426 chr1:166808415-166808428 chr1:166808415-166808428
5	CHD2	chr1:166808263-166808853	GM12878	blood:	n/a	n/a
6	YY1	chr1:166808422-166808841	GM12878	blood:	n/a	chr1:166808739-166808753
7	USF1	chr1:166808426-166808854	SK-N-SH	brain:	n/a	chr1:166808708-166808719
8	BHLHE40	chr1:166808346-166808854	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:166806518-166808834	K562	blood:	n/a	n/a
10	USF1	chr1:166808479-166808851	A549	lung:	n/a	chr1:166808708-166808719
11	POLR2A	chr1:166808232-166808897	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:166808146-166809567	K562	blood:	n/a	n/a
13	MAX	chr1:166808228-166808872	A549	lung:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166808709-166808718
14	HMGN3	chr1:166808318-166809519	K562	blood:	n/a	n/a
15	MYC	chr1:166808234-166808844	H1-hESC	embryonic stem cell:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166808709-166808718
16	TAF1	chr1:166808096-166808858	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr1:166808280-166808871	A549	lung:	n/a	n/a
18	HCFC1	chr1:166807862-166808929	Hela-S3	cervix:	n/a	n/a
19	USF1	chr1:166808617-166808829	HepG2	liver:	n/a	chr1:166808708-166808719
20	MXI1	chr1:166808205-166808846	K562	blood:	n/a	chr1:166808710-166808719
21	MYC	chr1:166808364-166808829	MCF-7	breast:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166808709-166808718
22	SP1	chr1:166808245-166808864	GM12878	blood:	n/a	chr1:166808510-166808519 chr1:166808720-166808734 chr1:166808697-166808711 chr1:166808506-166808515 chr1:166808653-166808667 chr1:166808511-166808520 chr1:166808511-166808520
23	PML	chr1:166808258-166808882	MCF-7	breast:	n/a	n/a
24	POLR2A	chr1:166808310-166808857	HepG2	liver:	n/a	n/a
25	GABPA	chr1:166808351-166808825	HepG2	liver:	n/a	chr1:166808814-166808823
26	POLR2A	chr1:166808234-166808899	HUVEC	blood vessel:	n/a	n/a
27	CTCF	chr1:166808395-166808851	K562	blood:	n/a	n/a
28	TCF7L2	chr1:166808174-166808812	Hela-S3	cervix:	n/a	n/a
29	YY1	chr1:166808280-166809369	GM12892	blood:	n/a	chr1:166809049-166809058 chr1:166809101-166809120 chr1:166809107-166809115 chr1:166808739-166808753
30	GABPA	chr1:166808204-166808857	K562	blood:	n/a	chr1:166808814-166808823
31	UBTF	chr1:166808157-166808898	K562	blood:	n/a	n/a
32	CBX3	chr1:166808008-166808896	K562	blood:	n/a	n/a
33	MYC	chr1:166808033-166808864	K562	blood:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166808709-166808718
34	POLR2A	chr1:166808195-166809672	IMR90	lung:	n/a	n/a
35	POLR2A	chr1:166808193-166809297	GM12878	blood:	n/a	n/a
36	MAZ	chr1:166807996-166809840	IMR90	lung:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166809214-166809224 chr1:166808709-166808718
37	POLR2A	chr1:166808236-166808898	U87	brain:	n/a	n/a
38	USF1	chr1:166808464-166808842	K562	blood:	n/a	chr1:166808708-166808719
39	POLR2A	chr1:166808197-166809160	HCT-116	colon:	n/a	n/a
40	MAX	chr1:166808186-166808929	SK-N-SH	brain:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166808709-166808718
41	HEY1	chr1:166808210-166808830	K562	blood:	n/a	chr1:166808815-166808830
42	HDAC2	chr1:166808336-166808821	HepG2	liver:	n/a	n/a
43	ELF1	chr1:166808131-166808840	K562	blood:	n/a	chr1:166808450-166808463
44	SIN3AK20	chr1:166808235-166808915	K562	blood:	n/a	n/a
45	POLR2A	chr1:166808210-166809417	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr1:166808206-166808972	GM12878	blood:	n/a	n/a
47	MYC	chr1:166808218-166809307	MCF-7	breast:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166809214-166809224 chr1:166808709-166808718
48	ZBTB7A	chr1:166808205-166808938	ECC-1	luminal epithelium:	n/a	n/a
49	TBL1XR1	chr1:166808377-166808850	GM12878	blood:	n/a	n/a
50	MAX	chr1:166808043-166809747	HCT-116	colon:	n/a	chr1:166808709-166808719 chr1:166808708-166808719 chr1:166808722-166808732 chr1:166808709-166808719 chr1:166809214-166809224 chr1:166808709-166808718

No.	Distal block	Cell Line	Cell type
1	chr1:166805232..166812474-chr1:166842359..166847542,11	MCF-7	breast:
2	chr1:166808183..166808891-chr2:88315947..88316502,2	Hela-S3	cervix:
3	chr1:166808293..166809161-chr19:2050789..2051603,2	Hela-S3	cervix:
4	chr1:166805959..166811139-chr1:166841080..166848642,15	MCF-7	breast:
5	chr1:165795265..165796893-chr1:166808551..166810494,2	K562	blood:
6	chr1:166807390..166809881-chr1:167187703..167190795,4	MCF-7	breast:
7	chr1:166806593..166810261-chr1:166844073..166846866,6	K562	blood:
8	chr1:166808237..166810193-chr1:166835815..166838073,2	MCF-7	breast:
9	chr1:166808391..166808920-chr1:202858119..202858926,2	Hela-S3	cervix:
10	chr1:166808206..166809091-chr15:72523170..72524154,2	Hela-S3	cervix:
11	chr1:166808599..166809122-chr15:59396935..59397740,2	Hela-S3	cervix:

Variant related genes	Relation type
POGK	TF binding region
ENSG00000225171	Chromatin interaction
ENSG00000157456	Chromatin interaction
ENSG00000143190	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000183155	Chromatin interaction
ENSG00000272205	Chromatin interaction
ENSG00000099875	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000152382	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv3344806	chr1:166807953-166810501	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a
3	esv3427862	chr1:166808053-166810151	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166807600-166809000	Active TSS	Brain Germinal Matrix	brain
2	chr1:166807600-166809600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:166807800-166809400	Active TSS	Fetal Muscle Trunk	muscle
4	chr1:166807800-166809600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr1:166807800-166809600	Active TSS	Psoas Muscle	Psoas
6	chr1:166807800-166810000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:166807800-166810400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:166808000-166809400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr1:166808000-166809400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:166808000-166809400	Active TSS	Brain Cingulate Gyrus	brain
11	chr1:166808000-166809400	Active TSS	Brain Hippocampus Middle	brain
12	chr1:166808000-166809400	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr1:166808000-166809400	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:166808000-166809400	Active TSS	Small Intestine	intestine
15	chr1:166808000-166809400	Active TSS	HSMM	muscle
16	chr1:166808000-166809600	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:166808000-166809600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:166808000-166809600	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:166808000-166809600	Active TSS	Fetal Brain Female	brain
20	chr1:166808000-166809600	Active TSS	Right Ventricle	heart
21	chr1:166808000-166809800	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:166808000-166809800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:166808000-166809800	Active TSS	Ovary	ovary
24	chr1:166808000-166809800	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr1:166808000-166810400	Active TSS	Aorta	Aorta
26	chr1:166808200-166809200	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr1:166808200-166809400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:166808200-166809400	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr1:166808200-166809400	Active TSS	Primary T cells from cord blood	blood
30	chr1:166808200-166809400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:166808200-166809400	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr1:166808200-166809400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:166808200-166809400	Active TSS	Brain Angular Gyrus	brain
34	chr1:166808200-166809400	Active TSS	Brain Substantia Nigra	brain
35	chr1:166808200-166809400	Active TSS	Colon Smooth Muscle	Colon
36	chr1:166808200-166809400	Active TSS	Fetal Intestine Large	intestine
37	chr1:166808200-166809400	Active TSS	Gastric	stomach
38	chr1:166808200-166809400	Active TSS	Placenta Amnion	Placenta Amnion
39	chr1:166808200-166809600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:166808200-166809600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:166808200-166809600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr1:166808200-166809600	Active TSS	HSMMtube	muscle
43	chr1:166808200-166809800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:166808200-166809800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:166808200-166809800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:166808200-166809800	Active TSS	Esophagus	oesophagus
47	chr1:166808200-166810000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:166808200-166810200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:166808200-166810200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:166808400-166809200	Active TSS	Primary B cells from cord blood	blood

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