Variant report

Variant	rs28450989
Chromosome Location	chr4:106630007-106630008
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:591)
CpG islands
(count:183)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:591 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr4:106629223-106630399	HCT-116	colon:	n/a	n/a
2	TAF1	chr4:106629565-106630044	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr4:106629450-106630435	MCF-7	breast:	n/a	n/a
4	MAX	chr4:106629492-106630331	A549	lung:	n/a	n/a
5	MAX	chr4:106629476-106630286	MCF-7	breast:	n/a	n/a
6	MYC	chr4:106628951-106630488	NB4	blood:	n/a	n/a
7	YY1	chr4:106629503-106630527	K562	blood:	n/a	n/a
8	ZC3H11A	chr4:106629600-106630128	K562	blood:	n/a	n/a
9	UBTF	chr4:106629661-106630537	K562	blood:	n/a	n/a
10	STAT5A	chr4:106629606-106630141	K562	blood:	n/a	n/a
11	CEBPB	chr4:106629700-106630041	H1-hESC	embryonic stem cell:	n/a	n/a
12	USF1	chr4:106629709-106630095	A549	lung:	n/a	n/a
13	POLR2A	chr4:106629046-106630707	HL-60	blood:	n/a	n/a
14	ETS1	chr4:106629579-106630168	A549	lung:	n/a	chr4:106629591-106629604
15	CEBPB	chr4:106629534-106630185	GM12878	blood:	n/a	n/a
16	SRF	chr4:106629693-106630011	GM12878	blood:	n/a	n/a
17	SIN3AK20	chr4:106629195-106630579	MCF-7	breast:	n/a	n/a
18	SIN3AK20	chr4:106629672-106630074	A549	lung:	n/a	n/a
19	SP1	chr4:106629478-106630300	HCT-116	colon:	n/a	chr4:106629899-106629908 chr4:106629897-106629908 chr4:106629800-106629812 chr4:106629800-106629812 chr4:106629801-106629810 chr4:106629898-106629907
20	POLR2A	chr4:106629561-106630512	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr4:106629083-106630441	K562	blood:	n/a	chr4:106630312-106630324
22	NFIC	chr4:106629279-106630371	GM12878	blood:	n/a	n/a
23	IRF4	chr4:106629585-106630107	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:106629416-106630352	HUVEC	blood vessel:	n/a	n/a
25	CUX1	chr4:106629701-106630031	K562	blood:	n/a	n/a
26	HEY1	chr4:106629324-106630303	K562	blood:	n/a	n/a
27	ETS1	chr4:106629535-106630134	K562	blood:	n/a	chr4:106629591-106629604
28	SIN3AK20	chr4:106629506-106630101	HepG2	liver:	n/a	n/a
29	GABPA	chr4:106629590-106630207	K562	blood:	n/a	n/a
30	POLR2A	chr4:106629252-106630359	GM12892	blood:	n/a	n/a
31	POLR2A	chr4:106629308-106630595	IMR90	lung:	n/a	n/a
32	POLR2A	chr4:106629580-106630222	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr4:106629423-106630527	K562	blood:	n/a	n/a
34	MEF2A	chr4:106629611-106630122	GM12878	blood:	n/a	n/a
35	ELF1	chr4:106629388-106630458	GM12878	blood:	n/a	n/a
36	TRIM28	chr4:106629478-106630188	K562	blood:	n/a	n/a
37	MYC	chr4:106629638-106630031	HepG2	liver:	n/a	n/a
38	PML	chr4:106629549-106630248	MCF-7	breast:	n/a	n/a
39	CCNT2	chr4:106629650-106630314	K562	blood:	n/a	chr4:106629898-106629907
40	EP300	chr4:106629655-106630009	K562	blood:	n/a	n/a
41	JUND	chr4:106629369-106630360	H1-hESC	embryonic stem cell:	n/a	n/a
42	CBX3	chr4:106629351-106630257	HCT-116	colon:	n/a	n/a
43	CREB1	chr4:106629261-106630343	HepG2	liver:	n/a	n/a
44	GABPA	chr4:106629365-106630507	HL-60	blood:	n/a	chr4:106629588-106629597
45	POLR2A	chr4:106629544-106630577	K562	blood:	n/a	n/a
46	RUNX3	chr4:106629345-106630162	GM12878	blood:	n/a	n/a
47	ETS1	chr4:106629589-106630134	GM12878	blood:	n/a	chr4:106629591-106629604
48	PAX5	chr4:106629519-106630216	GM12878	blood:	n/a	n/a
49	MEF2C	chr4:106629618-106630062	GM12878	blood:	n/a	n/a
50	TBL1XR1	chr4:106629574-106630055	GM12878	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:106629965-106630015	HCT-116	colon:	n/a
2	chr4:106629983-106630033	HCM	heart:	n/a
3	chr4:106629983-106630033	K562	blood:	n/a
4	chr4:106629962-106630012	CMK	blood:	n/a
5	chr4:106629983-106630033	MCF10A-Er-Src	breast:	n/a
6	chr4:106629962-106630012	BJ	skin:	n/a
7	chr4:106629965-106630015	Caco-2	colon:	n/a
8	chr4:106629962-106630012	SK-N-MC	brain:	n/a
9	chr4:106629962-106630012	SK-N-SH_RA	brain:	n/a
10	chr4:106629962-106630012	HCM	heart:	n/a
11	chr4:106629983-106630033	AoSMC	blood vessel:	n/a
12	chr4:106629962-106630012	PFSK-1	brain:	n/a
13	chr4:106629965-106630015	RPTEC	kidney:	n/a
14	chr4:106629983-106630033	CMK	blood:	n/a
15	chr4:106629983-106630033	LNCaP	prostate:	n/a
16	chr4:106629965-106630015	AG10803	skin:	n/a
17	chr4:106629983-106630033	HCF	heart:	n/a
18	chr4:106629965-106630015	HAEpiC	amniotic membrane:	n/a
19	chr4:106629965-106630015	BJ	skin:	n/a
20	chr4:106629965-106630015	H1-hESC	embryonic stem cell:	embryo
21	chr4:106629962-106630012	HEK293	kidney:	embryo
22	chr4:106629983-106630033	Caco-2	colon:	n/a
23	chr4:106629983-106630033	BJ	skin:	n/a
24	chr4:106629983-106630033	GM19239	blood:	n/a
25	chr4:106629965-106630015	Hepatocyte	liver:	n/a
26	chr4:106629983-106630033	GM06990	blood:	n/a
27	chr4:106629962-106630012	AG04450	lung:	fetal
28	chr4:106629965-106630015	HepG2	liver:	n/a
29	chr4:106629962-106630012	GM19239	blood:	n/a
30	chr4:106629965-106630015	SK-N-SH_RA	brain:	n/a
31	chr4:106629962-106630012	GM12891	blood:	n/a
32	chr4:106629983-106630033	H1-hESC	embryonic stem cell:	embryo
33	chr4:106629983-106630033	HIPEpiC	eye:	n/a
34	chr4:106629962-106630012	NHDF-neo	bronchial:	n/a
35	chr4:106629965-106630015	HIPEpiC	eye:	n/a
36	chr4:106629983-106630033	T-47D	breast:	n/a
37	chr4:106629965-106630015	MCF-7	breast:	n/a
38	chr4:106629965-106630015	PANC-1	pancreas:	n/a
39	chr4:106629983-106630033	AG09309	skin:	n/a
40	chr4:106629965-106630015	LNCaP	prostate:	n/a
41	chr4:106629962-106630012	ProgFib	skin:	n/a
42	chr4:106629965-106630015	U87	brain:	n/a
43	chr4:106629983-106630033	AG04450	lung:	fetal
44	chr4:106629962-106630012	GM06990	blood:	n/a
45	chr4:106629965-106630015	GM12878	blood:	n/a
46	chr4:106629983-106630033	NH-A	brain:	n/a
47	chr4:106629983-106630033	PANC-1	pancreas:	n/a
48	chr4:106629983-106630033	NHDF-neo	bronchial:	n/a
49	chr4:106629965-106630015	Jurkat	blood:	n/a
50	chr4:106629962-106630012	NT2-D1	testis:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:106394755..106397717-chr4:106629970..106632343,2	MCF-7	breast:
2	chr4:106628392..106631014-chr4:106816298..106818181,3	MCF-7	breast:
3	chr4:106628549..106631300-chr4:106636039..106639035,3	MCF-7	breast:
4	chr4:106393199..106396342-chr4:106628328..106631625,4	K562	blood:
5	chr4:106619847..106624541-chr4:106627186..106631133,7	MCF-7	breast:
6	chr4:106614729..106617409-chr4:106629462..106630998,2	MCF-7	breast:
7	chr20:58515297..58516040-chr4:106629913..106630788,2	HCT-116	colon:
8	chr4:106394828..106395492-chr4:106629382..106630203,2	K562	blood:
9	chr4:106393678..106396634-chr4:106628055..106631625,3	K562	blood:
10	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:
11	chr4:106628554..106633489-chr4:106634205..106639726,8	K562	blood:

No data

Variant related genes	Relation type
GSTCD	TF binding region
INTS12	TF binding region
INTS12	CpG island
GSTCD	CpG island
ENSG00000168743	Chromatin interaction
ENSG00000138777	Chromatin interaction
ENSG00000236699	Chromatin interaction
ENSG00000138780	Chromatin interaction
ENSG00000196227	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000132825	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10019217	0.85[ASN][1000 genomes]
rs10030620	0.80[ASN][1000 genomes]
rs10049527	0.82[ASN][1000 genomes]
rs10516522	1.00[ASN][1000 genomes]
rs11930244	0.87[ASN][1000 genomes]
rs11930965	0.90[ASN][1000 genomes]
rs11936611	0.82[ASN][1000 genomes]
rs12504088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511885	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512339	0.90[ASN][1000 genomes]
rs13110070	0.85[ASN][1000 genomes]
rs13145251	0.83[ASN][1000 genomes]
rs17036093	0.97[ASN][1000 genomes]
rs17036097	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17036102	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036158	0.92[ASN][1000 genomes]
rs17036254	0.82[ASN][1000 genomes]
rs2193852	0.92[ASN][1000 genomes]
rs2193853	0.92[ASN][1000 genomes]
rs28370551	1.00[ASN][1000 genomes]
rs28391170	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28559909	0.97[ASN][1000 genomes]
rs28698939	0.85[ASN][1000 genomes]
rs3796926	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4235415	0.87[ASN][1000 genomes]
rs4490460	1.00[ASN][1000 genomes]
rs4698950	0.93[ASN][1000 genomes]
rs4698951	0.92[ASN][1000 genomes]
rs4699192	0.85[ASN][1000 genomes]
rs4699193	1.00[ASN][1000 genomes]
rs4699194	1.00[ASN][1000 genomes]
rs4699195	1.00[ASN][1000 genomes]
rs4699197	1.00[ASN][1000 genomes]
rs4699198	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699199	0.92[ASN][1000 genomes]
rs58388061	0.95[ASN][1000 genomes]
rs58914657	0.83[ASN][1000 genomes]
rs59961848	0.84[ASN][1000 genomes]
rs60774107	0.97[ASN][1000 genomes]
rs60861135	0.92[ASN][1000 genomes]
rs6817029	0.88[ASN][1000 genomes]
rs6820671	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825379	0.82[ASN][1000 genomes]
rs6826631	0.82[ASN][1000 genomes]
rs6843771	0.82[ASN][1000 genomes]
rs7658055	0.82[ASN][1000 genomes]
rs7659526	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665588	0.92[ASN][1000 genomes]
rs7696836	0.85[ASN][1000 genomes]
rs7697619	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 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	chr4:106627800-106630800	Active TSS	GM12878-XiMat	blood
2	chr4:106628400-106631000	Active TSS	Psoas Muscle	Psoas
3	chr4:106628600-106630400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:106628600-106630400	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:106628600-106630800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr4:106628600-106630800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr4:106628600-106630800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr4:106628600-106630800	Active TSS	Aorta	Aorta
9	chr4:106628600-106630800	Active TSS	Ovary	ovary
10	chr4:106628600-106631000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:106628600-106631800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr4:106628800-106630200	Active TSS	Primary T cells fromperipheralblood	blood
13	chr4:106628800-106630200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:106628800-106630400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:106628800-106630400	Active TSS	Colonic Mucosa	Colon
16	chr4:106628800-106630800	Active TSS	Fetal Muscle Trunk	muscle
17	chr4:106628800-106630800	Active TSS	Left Ventricle	heart
18	chr4:106628800-106631000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:106628800-106631000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:106628800-106631000	Active TSS	Fetal Intestine Large	intestine
21	chr4:106628800-106631000	Active TSS	Fetal Muscle Leg	muscle
22	chr4:106628800-106631000	Active TSS	Fetal Thymus	thymus
23	chr4:106628800-106631000	Active TSS	Right Ventricle	heart
24	chr4:106628800-106631400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr4:106628800-106631400	Active TSS	A549	lung
26	chr4:106628800-106631600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:106628800-106631800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr4:106628800-106631800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr4:106629000-106630400	Active TSS	Fetal Lung	lung
30	chr4:106629000-106630400	Active TSS	Rectal Smooth Muscle	rectum
31	chr4:106629000-106630600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:106629000-106630600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:106629000-106630600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:106629000-106630600	Active TSS	Fetal Heart	heart
35	chr4:106629000-106630600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:106629000-106630600	Active TSS	Lung	lung
37	chr4:106629000-106630600	Active TSS	Pancreas	Pancrea
38	chr4:106629000-106630600	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr4:106629000-106630600	Active TSS	Stomach Mucosa	stomach
40	chr4:106629000-106630600	Active TSS	HSMMtube	muscle
41	chr4:106629000-106630800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr4:106629000-106630800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:106629000-106630800	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr4:106629000-106630800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:106629000-106630800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:106629000-106630800	Active TSS	Placenta Amnion	Placenta Amnion
47	chr4:106629000-106630800	Bivalent/Poised TSS	HepG2	liver
48	chr4:106629000-106630800	Active TSS	HSMM	muscle
49	chr4:106629000-106631000	Active TSS	Fetal Intestine Small	intestine
50	chr4:106629000-106631000	Active TSS	Fetal Kidney	kidney

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