Variant report

Variant	rs28613142
Chromosome Location	chr4:26322929-26322930
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	MAX	chr4:26320594-26322993	GM12878	blood:	n/a	chr4:26321515-26321525 chr4:26321518-26321528 chr4:26320772-26320782
2	POLR2A	chr4:26320536-26324309	IMR90	lung:	n/a	n/a
3	POLR2A	chr4:26321610-26322989	ECC-1	luminal epithelium:	n/a	n/a
4	HA-E2F1	chr4:26321937-26323138	Hela-S3	cervix:	n/a	chr4:26322262-26322271 chr4:26322507-26322517 chr4:26322533-26322543
5	YY1	chr4:26321626-26323288	GM12891	blood:	n/a	chr4:26322751-26322760 chr4:26322573-26322584 chr4:26322749-26322760 chr4:26323044-26323058 chr4:26322509-26322518 chr4:26322506-26322515 chr4:26322507-26322518
6	SIN3A	chr4:26320603-26324322	H1-hESC	embryonic stem cell:	n/a	chr4:26322924-26322935 chr4:26320763-26320772
7	MYC	chr4:26320618-26323066	K562	blood:	n/a	chr4:26321515-26321525 chr4:26321518-26321528 chr4:26320772-26320782
8	MAX	chr4:26320560-26323255	K562	blood:	n/a	chr4:26321515-26321525 chr4:26321518-26321528 chr4:26320772-26320782
9	TAF1	chr4:26320648-26323397	H1-hESC	embryonic stem cell:	n/a	n/a
10	HMGN3	chr4:26322042-26323227	K562	blood:	n/a	n/a
11	POLR2A	chr4:26320666-26323263	GM12878	blood:	n/a	n/a
12	TCF7L2	chr4:26322903-26323333	PANC-1	pancreas:	n/a	chr4:26323196-26323205
13	POLR2A	chr4:26320475-26323197	GM12892	blood:	n/a	n/a
14	CHD2	chr4:26320565-26323397	GM12878	blood:	n/a	chr4:26321233-26321242 chr4:26322612-26322621 chr4:26322485-26322495
15	YY1	chr4:26322083-26323040	K562	blood:	n/a	chr4:26322751-26322760 chr4:26322573-26322584 chr4:26322749-26322760 chr4:26322509-26322518 chr4:26322506-26322515 chr4:26322507-26322518
16	POLR2A	chr4:26320721-26323956	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr4:26320643-26323275	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:26320593-26322944	Hela-S3	cervix:	n/a	n/a
19	TCF7L2	chr4:26321212-26323742	Hela-S3	cervix:	n/a	chr4:26323196-26323205
20	CTCF	chr4:26322920-26323070	HMEC	breast:	n/a	chr4:26322968-26322981 chr4:26322965-26322978
21	POLR2A	chr4:26320553-26323344	HL-60	blood:	n/a	n/a
22	POLR2A	chr4:26322231-26322960	A549	lung:	n/a	n/a
23	CHD2	chr4:26320726-26323753	K562	blood:	n/a	chr4:26321233-26321242 chr4:26322612-26322621 chr4:26322485-26322495
24	POLR2A	chr4:26320632-26323237	GM18951	blood:	n/a	n/a
25	POLR2A	chr4:26322151-26322973	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr4:26322904-26323548	H1-hESC	embryonic stem cell:	n/a	n/a
27	CHD2	chr4:26320639-26323229	H1-hESC	embryonic stem cell:	n/a	chr4:26321233-26321242 chr4:26322612-26322621 chr4:26322485-26322495
28	JUN	chr4:26320429-26324200	K562	blood:	n/a	chr4:26320731-26320738 chr4:26323579-26323588 chr4:26321412-26321426 chr4:26320719-26320727 chr4:26320731-26320739
29	REST	chr4:26320592-26324055	H1-neurons	neurons:	n/a	chr4:26323177-26323190
30	POLR2A	chr4:26320610-26323804	GM19193	blood:	n/a	n/a
31	POLR2A	chr4:26322927-26323215	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr4:26320530-26323356	GM19099	blood:	n/a	n/a
33	MYC	chr4:26322739-26322987	MCF-7	breast:	n/a	n/a
34	POLR2A	chr4:26320633-26323144	K562	blood:	n/a	n/a
35	YY1	chr4:26320994-26323013	SK-N-SH	brain:	n/a	chr4:26322751-26322760 chr4:26322573-26322584 chr4:26322749-26322760 chr4:26321350-26321364 chr4:26322509-26322518 chr4:26322506-26322515 chr4:26322507-26322518
36	CTCF	chr4:26322920-26323070	GM12867	blood:	n/a	chr4:26322968-26322981 chr4:26322965-26322978
37	RCOR1	chr4:26320001-26323641	IMR90	lung:	n/a	n/a
38	TAF1	chr4:26322076-26323004	HepG2	liver:	n/a	n/a
39	YY1	chr4:26322096-26323187	HepG2	liver:	n/a	chr4:26322751-26322760 chr4:26322573-26322584 chr4:26322749-26322760 chr4:26323044-26323058 chr4:26322509-26322518 chr4:26322506-26322515 chr4:26322507-26322518
40	CCNT2	chr4:26320732-26323024	K562	blood:	n/a	chr4:26322572-26322581 chr4:26320949-26320958
41	EBF1	chr4:26322910-26323328	GM12878	blood:	n/a	n/a
42	UBTF	chr4:26322240-26323168	K562	blood:	n/a	n/a
43	YY1	chr4:26322077-26322936	ECC-1	luminal epithelium:	n/a	chr4:26322751-26322760 chr4:26322573-26322584 chr4:26322749-26322760 chr4:26322509-26322518 chr4:26322506-26322515 chr4:26322507-26322518
44	TBP	chr4:26320654-26323107	K562	blood:	n/a	n/a
45	UBTF	chr4:26320596-26323832	K562	blood:	n/a	n/a
46	POLR2A	chr4:26320511-26322967	K562	blood:	n/a	n/a
47	POLR2A	chr4:26320652-26322968	MCF-7	breast:	n/a	n/a
48	TAF1	chr4:26321905-26322936	ECC-1	luminal epithelium:	n/a	n/a
49	TCF7L2	chr4:26320536-26323340	HCT-116	colon:	n/a	chr4:26323196-26323205
50	POLR2A	chr4:26320576-26323982	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:73925667..73926363-chr4:26322580..26323106,2	Hela-S3	cervix:
2	chr4:25378479..25380375-chr4:26321026..26323579,2	K562	blood:
3	chr4:26319239..26325766-chr4:26360124..26364446,7	MCF-7	breast:

Variant related genes	Relation type
RBPJ	TF binding region
ENSG00000168214	Chromatin interaction
ENSG00000156642	Chromatin interaction
ENSG00000053900	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs28558703	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796802	0.88[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	nsv829889	chr4:26169954-26338313	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr4:26319800-26324800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:26320000-26323600	Active TSS	Rectal Smooth Muscle	rectum
3	chr4:26320000-26324200	Active TSS	Hela-S3	cervix
4	chr4:26320200-26323000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:26320200-26323800	Active TSS	K562	blood
6	chr4:26320200-26324000	Active TSS	A549	lung
7	chr4:26320200-26324400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:26320200-26324800	Active TSS	HSMMtube	muscle
9	chr4:26320200-26325200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:26320200-26326200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:26320400-26324200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:26320400-26324200	Active TSS	Fetal Intestine Large	intestine
13	chr4:26320400-26324400	Active TSS	HSMM	muscle
14	chr4:26320400-26324600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:26320400-26324600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr4:26320400-26324600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr4:26320400-26324600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:26320400-26324800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr4:26320400-26324800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:26320400-26325400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr4:26320400-26325400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:26320400-26326000	Active TSS	Fetal Brain Female	brain
23	chr4:26320600-26323000	Active TSS	Brain Germinal Matrix	brain
24	chr4:26320600-26323200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:26320600-26323200	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr4:26320600-26323200	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr4:26320600-26323200	Active TSS	Thymus	Thymus
28	chr4:26320600-26323400	Active TSS	Brain Hippocampus Middle	brain
29	chr4:26320600-26323400	Active TSS	Right Ventricle	heart
30	chr4:26320600-26323600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:26320600-26323600	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr4:26320600-26323600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:26320600-26323600	Active TSS	Brain Cingulate Gyrus	brain
34	chr4:26320600-26323600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:26320600-26323600	Active TSS	Esophagus	oesophagus
36	chr4:26320600-26323600	Active TSS	Lung	lung
37	chr4:26320600-26323600	Active TSS	Placenta Amnion	Placenta Amnion
38	chr4:26320600-26323600	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr4:26320600-26323800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr4:26320600-26323800	Active TSS	Brain Substantia Nigra	brain
41	chr4:26320600-26323800	Active TSS	Colon Smooth Muscle	Colon
42	chr4:26320600-26323800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr4:26320600-26323800	Active TSS	Fetal Intestine Small	intestine
44	chr4:26320600-26323800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr4:26320600-26323800	Active TSS	Small Intestine	intestine
46	chr4:26320600-26323800	Active TSS	NHEK	skin
47	chr4:26320600-26324000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:26320600-26324000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:26320600-26324000	Active TSS	Aorta	Aorta
50	chr4:26320600-26324000	Active TSS	Fetal Lung	lung

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