Variant report

Variant	rs28403197
Chromosome Location	chr4:106629567-106629568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:308)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:308 , 50 per page) page: 1 2 3 4 5 6 7

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	POLR2A	chr4:106629046-106630707	HL-60	blood:	n/a	n/a
9	CEBPB	chr4:106629534-106630185	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr4:106629195-106630579	MCF-7	breast:	n/a	n/a
11	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
12	POLR2A	chr4:106629561-106630512	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr4:106629083-106630441	K562	blood:	n/a	chr4:106630312-106630324
14	NFIC	chr4:106629279-106630371	GM12878	blood:	n/a	n/a
15	POLR2A	chr4:106629416-106630352	HUVEC	blood vessel:	n/a	n/a
16	HEY1	chr4:106629324-106630303	K562	blood:	n/a	n/a
17	ETS1	chr4:106629535-106630134	K562	blood:	n/a	chr4:106629591-106629604
18	SIN3AK20	chr4:106629506-106630101	HepG2	liver:	n/a	n/a
19	POLR2A	chr4:106629252-106630359	GM12892	blood:	n/a	n/a
20	POLR2A	chr4:106629308-106630595	IMR90	lung:	n/a	n/a
21	POLR2A	chr4:106629423-106630527	K562	blood:	n/a	n/a
22	ELF1	chr4:106629388-106630458	GM12878	blood:	n/a	n/a
23	TRIM28	chr4:106629478-106630188	K562	blood:	n/a	n/a
24	PML	chr4:106629549-106630248	MCF-7	breast:	n/a	n/a
25	JUND	chr4:106629369-106630360	H1-hESC	embryonic stem cell:	n/a	n/a
26	CBX3	chr4:106629351-106630257	HCT-116	colon:	n/a	n/a
27	CREB1	chr4:106629261-106630343	HepG2	liver:	n/a	n/a
28	GABPA	chr4:106629365-106630507	HL-60	blood:	n/a	chr4:106629588-106629597
29	POLR2A	chr4:106629544-106630577	K562	blood:	n/a	n/a
30	RUNX3	chr4:106629345-106630162	GM12878	blood:	n/a	n/a
31	PAX5	chr4:106629519-106630216	GM12878	blood:	n/a	n/a
32	CTBP2	chr4:106629302-106630496	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:106629268-106630542	HEK293	kidney:	n/a	n/a
34	TAF1	chr4:106629517-106630302	H1-neurons	neurons:	n/a	n/a
35	MAX	chr4:106629302-106630509	HepG2	liver:	n/a	n/a
36	TBP	chr4:106629185-106630644	Hela-S3	cervix:	n/a	n/a
37	TBP	chr4:106629046-106630581	K562	blood:	n/a	n/a
38	EP300	chr4:106629485-106630312	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr4:106629293-106630694	K562	blood:	n/a	n/a
40	POLR2A	chr4:106629408-106630712	Hela-S3	cervix:	n/a	n/a
41	SIN3AK20	chr4:106629274-106630002	H1-hESC	embryonic stem cell:	n/a	n/a
42	SMARCB1	chr4:106629508-106630560	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr4:106629345-106630647	H1-hESC	embryonic stem cell:	n/a	n/a
44	GABPA	chr4:106629448-106630422	MCF-7	breast:	n/a	chr4:106629588-106629597
45	RELA	chr4:106629193-106630118	GM19099	blood:	n/a	n/a
46	MAX	chr4:106629508-106630329	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr4:106629226-106630450	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr4:106629504-106630201	GM12892	blood:	n/a	n/a
49	POLR2A	chr4:106629332-106630441	HepG2	liver:	n/a	n/a
50	POLR2A	chr4:106629512-106630300	A549	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:106600442..106602529-chr4:106626797..106629772,2	K562	blood:
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	chr4:106394828..106395492-chr4:106629382..106630203,2	K562	blood:
8	chr4:106393678..106396634-chr4:106628055..106631625,3	K562	blood:
9	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:
10	chr4:106628554..106633489-chr4:106634205..106639726,8	K562	blood:

No data

Variant related genes	Relation type
GSTCD	TF binding region
INTS12	TF binding region
ENSG00000248778	Chromatin interaction
ENSG00000138780	Chromatin interaction
ENSG00000168743	Chromatin interaction
ENSG00000138777	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000236699	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10009875	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013631	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10026561	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28414565	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28642176	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4434257	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs61526371	1.00[EUR][1000 genomes]
rs61736388	1.00[EUR][1000 genomes]
rs9991722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][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	chr4:106628000-106629800	Active TSS	Right Atrium	heart
3	chr4:106628400-106629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:106628400-106631000	Active TSS	Psoas Muscle	Psoas
5	chr4:106628600-106629600	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr4:106628600-106629600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:106628600-106629600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr4:106628600-106630400	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr4:106628600-106630400	Active TSS	Stomach Smooth Muscle	stomach
10	chr4:106628600-106630800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr4:106628600-106630800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:106628600-106630800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:106628600-106630800	Active TSS	Aorta	Aorta
14	chr4:106628600-106630800	Active TSS	Ovary	ovary
15	chr4:106628600-106631000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:106628600-106631800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:106628800-106629600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr4:106628800-106629600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr4:106628800-106629600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr4:106628800-106629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:106628800-106629600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr4:106628800-106630200	Active TSS	Primary T cells fromperipheralblood	blood
23	chr4:106628800-106630200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:106628800-106630400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:106628800-106630400	Active TSS	Colonic Mucosa	Colon
26	chr4:106628800-106630800	Active TSS	Fetal Muscle Trunk	muscle
27	chr4:106628800-106630800	Active TSS	Left Ventricle	heart
28	chr4:106628800-106631000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:106628800-106631000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:106628800-106631000	Active TSS	Fetal Intestine Large	intestine
31	chr4:106628800-106631000	Active TSS	Fetal Muscle Leg	muscle
32	chr4:106628800-106631000	Active TSS	Fetal Thymus	thymus
33	chr4:106628800-106631000	Active TSS	Right Ventricle	heart
34	chr4:106628800-106631400	Active TSS	H1 Cell Line	embryonic stem cell
35	chr4:106628800-106631400	Active TSS	A549	lung
36	chr4:106628800-106631600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:106628800-106631800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr4:106628800-106631800	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr4:106629000-106629600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr4:106629000-106630400	Active TSS	Fetal Lung	lung
41	chr4:106629000-106630400	Active TSS	Rectal Smooth Muscle	rectum
42	chr4:106629000-106630600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:106629000-106630600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:106629000-106630600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:106629000-106630600	Active TSS	Fetal Heart	heart
46	chr4:106629000-106630600	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr4:106629000-106630600	Active TSS	Lung	lung
48	chr4:106629000-106630600	Active TSS	Pancreas	Pancrea
49	chr4:106629000-106630600	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr4:106629000-106630600	Active TSS	Stomach Mucosa	stomach

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