Variant report

Variant	rs3796802
Chromosome Location	chr4:26321784-26321785
allele	C/G
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	CTCF	chr4:26321720-26321870	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr4:26320152-26322795	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr4:26320515-26322824	GM12892	blood:	n/a	n/a
5	POLR2A	chr4:26320536-26324309	IMR90	lung:	n/a	n/a
6	POLR2A	chr4:26321610-26322989	ECC-1	luminal epithelium:	n/a	n/a
7	BRCA1	chr4:26320664-26322039	Hela-S3	cervix:	n/a	chr4:26321233-26321242
8	RCOR1	chr4:26320567-26322804	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:26320593-26322899	GM12891	blood:	n/a	n/a
10	MXI1	chr4:26320694-26322716	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr4:26321721-26322657	K562	blood:	n/a	n/a
12	ELF1	chr4:26321257-26321784	K562	blood:	n/a	chr4:26321622-26321631 chr4:26321583-26321594 chr4:26321582-26321595 chr4:26321584-26321593
13	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
14	SIN3A	chr4:26320603-26324322	H1-hESC	embryonic stem cell:	n/a	chr4:26322924-26322935 chr4:26320763-26320772
15	CTBP2	chr4:26320822-26322564	H1-hESC	embryonic stem cell:	n/a	n/a
16	RUNX3	chr4:26320549-26322839	GM12878	blood:	n/a	n/a
17	MYC	chr4:26320587-26322863	K562	blood:	n/a	chr4:26321515-26321525 chr4:26321518-26321528 chr4:26320772-26320782
18	YY1	chr4:26321157-26322853	H1-hESC	embryonic stem cell:	n/a	chr4:26322751-26322760 chr4:26322573-26322584 chr4:26322749-26322760 chr4:26321350-26321364 chr4:26322509-26322518 chr4:26322506-26322515 chr4:26322507-26322518
19	SIN3AK20	chr4:26320507-26321790	MCF-7	breast:	n/a	n/a
20	POLR2A	chr4:26321428-26322756	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr4:26320605-26322837	GM12878	blood:	n/a	n/a
22	MAX	chr4:26320305-26322870	NB4	blood:	n/a	chr4:26321515-26321525 chr4:26321518-26321528 chr4:26320772-26320782
23	ELF1	chr4:26320585-26322897	GM12878	blood:	n/a	chr4:26321622-26321631 chr4:26320768-26320777 chr4:26322509-26322518 chr4:26320769-26320781 chr4:26321583-26321594 chr4:26321582-26321595 chr4:26321584-26321593 chr4:26322506-26322515
24	MYC	chr4:26320618-26323066	K562	blood:	n/a	chr4:26321515-26321525 chr4:26321518-26321528 chr4:26320772-26320782
25	MAX	chr4:26320560-26323255	K562	blood:	n/a	chr4:26321515-26321525 chr4:26321518-26321528 chr4:26320772-26320782
26	TAF1	chr4:26320648-26323397	H1-hESC	embryonic stem cell:	n/a	n/a
27	RCOR1	chr4:26320591-26322761	K562	blood:	n/a	n/a
28	USF2	chr4:26321743-26322324	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:26320666-26323263	GM12878	blood:	n/a	n/a
30	RELA	chr4:26320603-26322679	GM18505	blood:	n/a	n/a
31	POLR2A	chr4:26320475-26323197	GM12892	blood:	n/a	n/a
32	TEAD4	chr4:26320761-26321893	ECC-1	luminal epithelium:	n/a	n/a
33	E2F6	chr4:26320628-26322749	H1-hESC	embryonic stem cell:	n/a	chr4:26322262-26322271 chr4:26322507-26322517 chr4:26322533-26322543 chr4:26320771-26320780 chr4:26321200-26321211 chr4:26320778-26320787
34	POLR2A	chr4:26321585-26321816	Gliobla	brain:	n/a	n/a
35	MTA3	chr4:26321644-26322394	GM12878	blood:	n/a	n/a
36	CHD2	chr4:26320565-26323397	GM12878	blood:	n/a	chr4:26321233-26321242 chr4:26322612-26322621 chr4:26322485-26322495
37	POLR2A	chr4:26320721-26323956	H1-neurons	neurons:	n/a	n/a
38	POU2F2	chr4:26321591-26322774	GM12891	blood:	n/a	chr4:26322001-26322013
39	POLR2A	chr4:26320643-26323275	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:26320593-26322944	Hela-S3	cervix:	n/a	n/a
41	PAX5	chr4:26320436-26322363	GM12878	blood:	n/a	n/a
42	PAX5	chr4:26321725-26322105	GM12891	blood:	n/a	n/a
43	TCF7L2	chr4:26321236-26322513	PANC-1	pancreas:	n/a	n/a
44	YY1	chr4:26320730-26321954	K562	blood:	n/a	chr4:26321350-26321364
45	TCF7L2	chr4:26321212-26323742	Hela-S3	cervix:	n/a	chr4:26323196-26323205
46	TBL1XR1	chr4:26321098-26322792	K562	blood:	n/a	n/a
47	RAD21	chr4:26320669-26322629	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF12	chr4:26320566-26321857	A549	lung:	n/a	chr4:26320864-26320874 chr4:26321692-26321699
49	POLR2A	chr4:26320553-26323344	HL-60	blood:	n/a	n/a
50	NFIC	chr4:26321682-26322696	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:25378479..25380375-chr4:26321026..26323579,2	K562	blood:
2	chr4:25914401..25916175-chr4:26320738..26322461,2	K562	blood:
3	chr1:111505715..111506419-chr4:26321647..26322451,2	Hela-S3	cervix:
4	chr12:123011205..123011721-chr4:26321688..26322554,2	Hela-S3	cervix:
5	chr4:26319239..26325766-chr4:26360124..26364446,7	MCF-7	breast:

Variant related genes	Relation type
RBPJ	TF binding region
ENSG00000168214	Chromatin interaction
ENSG00000053900	Chromatin interaction
ENSG00000250317	Chromatin interaction
ENSG00000273010	Chromatin interaction
ENSG00000111011	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10015035	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13144133	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17644283	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28558703	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28613142	0.88[ASN][1000 genomes]
rs6844659	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[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	chr4:26320000-26322400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:26320000-26323600	Active TSS	Rectal Smooth Muscle	rectum
4	chr4:26320000-26324200	Active TSS	Hela-S3	cervix
5	chr4:26320200-26323000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:26320200-26323800	Active TSS	K562	blood
7	chr4:26320200-26324000	Active TSS	A549	lung
8	chr4:26320200-26324400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:26320200-26324800	Active TSS	HSMMtube	muscle
10	chr4:26320200-26325200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:26320200-26326200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:26320400-26321800	Active TSS	Duodenum Mucosa	Duodenum
13	chr4:26320400-26321800	Active TSS	Osteobl	bone
14	chr4:26320400-26324200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:26320400-26324200	Active TSS	Fetal Intestine Large	intestine
16	chr4:26320400-26324400	Active TSS	HSMM	muscle
17	chr4:26320400-26324600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:26320400-26324600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr4:26320400-26324600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:26320400-26324600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:26320400-26324800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:26320400-26324800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:26320400-26325400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr4:26320400-26325400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:26320400-26326000	Active TSS	Fetal Brain Female	brain
26	chr4:26320600-26321800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr4:26320600-26321800	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr4:26320600-26321800	Active TSS	NHLF	lung
29	chr4:26320600-26322200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:26320600-26323000	Active TSS	Brain Germinal Matrix	brain
31	chr4:26320600-26323200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:26320600-26323200	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr4:26320600-26323200	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr4:26320600-26323200	Active TSS	Thymus	Thymus
35	chr4:26320600-26323400	Active TSS	Brain Hippocampus Middle	brain
36	chr4:26320600-26323400	Active TSS	Right Ventricle	heart
37	chr4:26320600-26323600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:26320600-26323600	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr4:26320600-26323600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:26320600-26323600	Active TSS	Brain Cingulate Gyrus	brain
41	chr4:26320600-26323600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:26320600-26323600	Active TSS	Esophagus	oesophagus
43	chr4:26320600-26323600	Active TSS	Lung	lung
44	chr4:26320600-26323600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr4:26320600-26323600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr4:26320600-26323800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr4:26320600-26323800	Active TSS	Brain Substantia Nigra	brain
48	chr4:26320600-26323800	Active TSS	Colon Smooth Muscle	Colon
49	chr4:26320600-26323800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr4:26320600-26323800	Active TSS	Fetal Intestine Small	intestine

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