Variant report

Variant	rs4252749
Chromosome Location	chr4:77997658-77997659
allele	C/T
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	ELF1	chr4:77997055-77997719	SK-N-SH	brain:	n/a	chr4:77997104-77997113 chr4:77997484-77997496 chr4:77997251-77997264
2	POU2F2	chr4:77996489-77998031	GM12878	blood:	n/a	chr4:77996944-77996956
3	POLR2A	chr4:77996934-77997941	Hela-S3	cervix:	n/a	n/a
4	PAX5	chr4:77997050-77997706	GM12878	blood:	n/a	n/a
5	TAF1	chr4:77996934-77997863	K562	blood:	n/a	n/a
6	POU2F2	chr4:77996953-77997774	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:77996102-77998071	H1-neurons	neurons:	n/a	n/a
8	ZBTB7A	chr4:77996208-77997739	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr4:77997074-77997936	NB4	blood:	n/a	n/a
10	MYBL2	chr4:77996952-77997710	HepG2	liver:	n/a	n/a
11	TAF1	chr4:77996940-77997764	GM12891	blood:	n/a	n/a
12	MAX	chr4:77996957-77997824	ECC-1	luminal epithelium:	n/a	chr4:77996958-77996968
13	POLR2A	chr4:77996979-77997812	HepG2	liver:	n/a	n/a
14	PML	chr4:77996526-77998140	GM12878	blood:	n/a	n/a
15	ARID3A	chr4:77997216-77997914	K562	blood:	n/a	n/a
16	POLR2A	chr4:77996629-77997880	PANC-1	pancreas:	n/a	n/a
17	POU2F2	chr4:77996969-77997814	GM12891	blood:	n/a	n/a
18	MYC	chr4:77996277-77998016	NB4	blood:	n/a	chr4:77996878-77996888 chr4:77996958-77996968
19	SIN3AK20	chr4:77996929-77997869	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:77996202-77997940	SK-N-SH	brain:	n/a	n/a
21	MXI1	chr4:77996187-77997724	HepG2	liver:	n/a	n/a
22	CHD2	chr4:77996984-77997720	HepG2	liver:	n/a	chr4:77997025-77997035
23	CEBPB	chr4:77997269-77997782	K562	blood:	n/a	n/a
24	MAFK	chr4:77997160-77997887	HepG2	liver:	n/a	chr4:77997861-77997872 chr4:77997862-77997873 chr4:77997355-77997370
25	POLR2A	chr4:77996562-77997926	SK-N-MC	brain:	n/a	n/a
26	ZNF384	chr4:77996843-77997714	GM12878	blood:	n/a	n/a
27	GTF2F1	chr4:77997051-77997786	H1-hESC	embryonic stem cell:	n/a	n/a
28	EP300	chr4:77996671-77997922	GM12878	blood:	n/a	chr4:77996891-77996900 chr4:77996944-77996953 chr4:77997214-77997227
29	POLR2A	chr4:77995775-77998045	GM12878	blood:	n/a	n/a
30	SP1	chr4:77996931-77997860	H1-hESC	embryonic stem cell:	n/a	chr4:77997545-77997559 chr4:77997183-77997195 chr4:77997183-77997195 chr4:77997026-77997035 chr4:77997549-77997558 chr4:77996953-77996967
31	MYC	chr4:77997067-77997816	K562	blood:	n/a	n/a
32	JUND	chr4:77996967-77997664	A549	lung:	n/a	chr4:77997446-77997455
33	CEBPB	chr4:77996951-77997912	GM12878	blood:	n/a	n/a
34	RELA	chr4:77996621-77997816	GM12892	blood:	n/a	n/a
35	POLR2A	chr4:77996152-77997843	HCT-116	colon:	n/a	n/a
36	BCL11A	chr4:77997011-77997915	GM12878	blood:	n/a	chr4:77997266-77997279
37	POLR2A	chr4:77996197-77997952	MCF-7	breast:	n/a	n/a
38	JUND	chr4:77996873-77997914	HCT-116	colon:	n/a	chr4:77997446-77997455
39	POLR2A	chr4:77996124-77998044	H1-neurons	neurons:	n/a	n/a
40	TCF7L2	chr4:77997059-77997700	Hela-S3	cervix:	n/a	n/a
41	RELA	chr4:77996930-77998007	GM18505	blood:	n/a	n/a
42	MAX	chr4:77997052-77997786	K562	blood:	n/a	n/a
43	BHLHE40	chr4:77997071-77997712	HepG2	liver:	n/a	n/a
44	TCF12	chr4:77996978-77997980	ECC-1	luminal epithelium:	n/a	n/a
45	MAZ	chr4:77996130-77998048	IMR90	lung:	n/a	chr4:77996254-77996264 chr4:77996878-77996888 chr4:77996958-77996968
46	POLR2A	chr4:77996392-77997779	HepG2	liver:	n/a	n/a
47	FOXA1	chr4:77997032-77997771	HepG2	liver:	n/a	n/a
48	BCL3	chr4:77996950-77997729	A549	lung:	n/a	chr4:77997266-77997279
49	JUND	chr4:77996187-77998103	GM12878	blood:	n/a	chr4:77997446-77997455
50	MAFK	chr4:77997143-77997791	HepG2	liver:	n/a	chr4:77997355-77997370

No.	Distal block	Cell Line	Cell type
1	chr4:77869773..77871632-chr4:77995514..77998178,4	K562	blood:
2	chr4:77993925..77999822-chr4:78072652..78081114,32	MCF-7	breast:
3	chr4:77975545..77980821-chr4:77994993..77998408,5	MCF-7	breast:
4	chr4:77973346..77979214-chr4:77995835..77998143,7	K562	blood:
5	chr4:77994543..78000148-chr4:78076403..78082799,9	K562	blood:
6	chr2:38603849..38604704-chr4:77996979..77997834,2	Hela-S3	cervix:
7	chr14:39639468..39640157-chr4:77997435..77998034,2	NB4	blood:
8	chr4:77995405..77999334-chr4:78000731..78006327,9	MCF-7	breast:
9	chr4:77997037..77997823-chr7:44621437..44622275,2	NB4	blood:
10	chr4:77869773..77872075-chr4:77995627..77998726,3	K562	blood:
11	chr4:77994285..77999121-chr4:78003590..78007383,5	K562	blood:
12	chr4:77994107..77999899-chr4:78076204..78082875,32	MCF-7	breast:
13	chr4:77870359..77873653-chr4:77995177..77998877,4	MCF-7	breast:
14	chr4:77995650..77999094-chr4:78076501..78080726,6	K562	blood:
15	chr4:77995679..77998060-chr4:78068555..78071849,3	K562	blood:
16	chr4:77975437..77978394-chr4:77996359..77998684,2	MCF-7	breast:
17	chr4:77997074..77997728-chr6:26056445..26056982,2	HCT-116	colon:
18	chr4:77979701..77986849-chr4:77990863..77998763,10	MCF-7	breast:
19	chr4:77996001..77999161-chr4:78070349..78073053,3	K562	blood:
20	chr4:77977102..77979783-chr4:77995512..77998143,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEPT11-2	chr4:77997130-77999849	NONHSAT097041

Variant related genes	Relation type
CCNI	TF binding region
ENSG00000119787	Chromatin interaction
ENSG00000138764	Chromatin interaction
ENSG00000214062	Chromatin interaction
ENSG00000201641	Chromatin interaction
ENSG00000158604	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000182400	Chromatin interaction
ENSG00000118816	Chromatin interaction
ENSG00000138758	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17002342	1.00[AMR][1000 genomes]
rs17002354	1.00[AMR][1000 genomes]
rs4252775	1.00[AMR][1000 genomes]
rs4252791	1.00[AMR][1000 genomes]
rs4252812	1.00[AMR][1000 genomes]
rs4252859	1.00[AMR][1000 genomes]
rs4252934	1.00[AMR][1000 genomes]
rs4252939	1.00[AMR][1000 genomes]
rs4252944	1.00[AMR][1000 genomes]
rs4252945	1.00[AMR][1000 genomes]
rs4476626	1.00[AMR][1000 genomes]
rs57303670	1.00[AMR][1000 genomes]
rs60458841	1.00[AMR][1000 genomes]
rs73826493	1.00[AMR][1000 genomes]
rs73826720	1.00[AMR][1000 genomes]
rs73826723	1.00[AMR][1000 genomes]
rs73829817	1.00[AMR][1000 genomes]
rs7690082	1.00[AMR][1000 genomes]

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	nsv879499	chr4:77990904-78003416	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv3330627	chr4:77995278-77997926	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3357193	chr4:77995453-77998301	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr4:77992000-77998200	Active TSS	GM12878-XiMat	blood
2	chr4:77993600-77998200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr4:77993600-77998400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:77993800-77998600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:77994000-77997800	Active TSS	Ovary	ovary
6	chr4:77994000-77998000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:77994000-77998400	Active TSS	Aorta	Aorta
8	chr4:77994000-77998600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr4:77994200-77998000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:77994200-77998000	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr4:77994200-77998000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:77994200-77998200	Active TSS	HSMMtube	muscle
13	chr4:77994200-77998200	Active TSS	NHDF-Ad	bronchial
14	chr4:77994400-77998000	Active TSS	Left Ventricle	heart
15	chr4:77994400-77998000	Active TSS	Right Ventricle	heart
16	chr4:77994400-77998200	Active TSS	Fetal Muscle Trunk	muscle
17	chr4:77994400-77998800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:77994400-77998800	Active TSS	Rectal Smooth Muscle	rectum
19	chr4:77994600-77998200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr4:77994600-77998200	Active TSS	Primary T cells fromperipheralblood	blood
21	chr4:77994600-77998400	Active TSS	Brain Germinal Matrix	brain
22	chr4:77994600-77998600	Active TSS	Stomach Smooth Muscle	stomach
23	chr4:77994600-77998800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr4:77994800-77997800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:77994800-77997800	Active TSS	NHEK	skin
26	chr4:77994800-77998000	Active TSS	Colonic Mucosa	Colon
27	chr4:77994800-77998000	Active TSS	Esophagus	oesophagus
28	chr4:77994800-77998000	Active TSS	Fetal Intestine Small	intestine
29	chr4:77994800-77998200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:77994800-77998200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:77995000-77997800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:77995000-77997800	Active TSS	HMEC	breast
33	chr4:77995000-77998000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:77995000-77998000	Active TSS	Brain Substantia Nigra	brain
35	chr4:77995000-77998200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:77995000-77998200	Active TSS	Fetal Brain Male	brain
37	chr4:77995000-77998200	Active TSS	Fetal Brain Female	brain
38	chr4:77995000-77998200	Active TSS	Fetal Thymus	thymus
39	chr4:77995000-77998200	Active TSS	K562	blood
40	chr4:77995000-77998400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:77995000-77998400	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr4:77995000-77998400	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr4:77995000-77998400	Active TSS	HSMM	muscle
44	chr4:77995000-77998400	Active TSS	NHLF	lung
45	chr4:77995000-77998600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr4:77995200-77997800	Active TSS	Muscle Satellite Cultured Cells	--
47	chr4:77995200-77998000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:77995200-77998200	Active TSS	Fetal Intestine Large	intestine
49	chr4:77995200-77998400	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr4:77995200-77998400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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