Variant report

Variant	rs3822223
Chromosome Location	chr4:26321906-26321907
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	chr4:26320152-26322795	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr4:26320515-26322824	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:26320536-26324309	IMR90	lung:	n/a	n/a
5	POLR2A	chr4:26321610-26322989	ECC-1	luminal epithelium:	n/a	n/a
6	BRCA1	chr4:26320664-26322039	Hela-S3	cervix:	n/a	chr4:26321233-26321242
7	RCOR1	chr4:26320567-26322804	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:26320593-26322899	GM12891	blood:	n/a	n/a
9	HEY1	chr4:26321849-26322844	K562	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	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
13	SIN3A	chr4:26320603-26324322	H1-hESC	embryonic stem cell:	n/a	chr4:26322924-26322935 chr4:26320763-26320772
14	CTBP2	chr4:26320822-26322564	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr4:26321905-26322002	K562	blood:	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	CTCF	chr4:26321820-26321970	WERI-Rb-1	eye:	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	CTCF	chr4:26321800-26321950	HRPEpiC	eye:	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	MTA3	chr4:26321644-26322394	GM12878	blood:	n/a	n/a
35	CHD2	chr4:26320565-26323397	GM12878	blood:	n/a	chr4:26321233-26321242 chr4:26322612-26322621 chr4:26322485-26322495
36	EP300	chr4:26321889-26322525	GM12878	blood:	n/a	chr4:26322507-26322523 chr4:26322508-26322517 chr4:26322479-26322488
37	BCL3	chr4:26321798-26322418	GM12878	blood:	n/a	n/a
38	POLR2A	chr4:26320721-26323956	H1-neurons	neurons:	n/a	n/a
39	POU2F2	chr4:26321591-26322774	GM12891	blood:	n/a	chr4:26322001-26322013
40	POLR2A	chr4:26320643-26323275	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:26320593-26322944	Hela-S3	cervix:	n/a	n/a
42	PAX5	chr4:26320436-26322363	GM12878	blood:	n/a	n/a
43	PAX5	chr4:26321725-26322105	GM12891	blood:	n/a	n/a
44	TCF7L2	chr4:26321236-26322513	PANC-1	pancreas:	n/a	n/a
45	YY1	chr4:26320730-26321954	K562	blood:	n/a	chr4:26321350-26321364
46	TCF7L2	chr4:26321212-26323742	Hela-S3	cervix:	n/a	chr4:26323196-26323205
47	TBL1XR1	chr4:26321098-26322792	K562	blood:	n/a	n/a
48	EP300	chr4:26321855-26322552	GM12878	blood:	n/a	chr4:26322507-26322523 chr4:26322508-26322517 chr4:26322479-26322488
49	RAD21	chr4:26320669-26322629	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr4:26320553-26323344	HL-60	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:26321873-26321923	SAEC	small airway:	n/a
2	chr4:26321873-26321923	SK-N-SH	brain:	n/a
3	chr4:26321873-26321923	HMEC	breast:	n/a
4	chr4:26321873-26321923	K562	blood:	n/a
5	chr4:26321873-26321923	AG09309	skin:	n/a
6	chr4:26321873-26321923	BJ	skin:	n/a
7	chr4:26321873-26321923	AG09319	gingival:	n/a
8	chr4:26321873-26321923	HNPCEpiC	eye:	n/a
9	chr4:26321873-26321923	GM12891	blood:	n/a
10	chr4:26321873-26321923	GM12878	blood:	n/a
11	chr4:26321873-26321923	NHBE	bronchial:	n/a
12	chr4:26321873-26321923	HRPEpiC	eye:	n/a
13	chr4:26321873-26321923	H1-hESC	embryonic stem cell:	embryo
14	chr4:26321873-26321923	U87	brain:	n/a
15	chr4:26321873-26321923	PFSK-1	brain:	n/a
16	chr4:26321873-26321923	NB4	blood:	n/a
17	chr4:26321873-26321923	Caco-2	colon:	n/a
18	chr4:26321873-26321923	ProgFib	skin:	n/a
19	chr4:26321873-26321923	IMR90	lung:	fetal
20	chr4:26321873-26321923	GM12892	blood:	n/a
21	chr4:26321873-26321923	GM06990	blood:	n/a
22	chr4:26321873-26321923	NT2-D1	testis:	n/a
23	chr4:26321873-26321923	SK-N-SH_RA	brain:	n/a
24	chr4:26321873-26321923	ovcar-3	ovarian:	n/a
25	chr4:26321873-26321923	T-47D	breast:	n/a
26	chr4:26321873-26321923	HCPEpiC	choroid plexus:	n/a
27	chr4:26321873-26321923	HEK293	kidney:	embryo
28	chr4:26321873-26321923	GM19239	blood:	n/a
29	chr4:26321873-26321923	AG04449	skin:	fetal
30	chr4:26321873-26321923	NHDF-neo	bronchial:	n/a
31	chr4:26321873-26321923	Hela-S3	cervix:	n/a
32	chr4:26321873-26321923	BE2_C	brain:	n/a
33	chr4:26321873-26321923	HCT-116	colon:	n/a
34	chr4:26321873-26321923	HEEpiC	esophagus:	n/a
35	chr4:26321873-26321923	PrEC	prostate:	n/a
36	chr4:26321873-26321923	SKMC	muscle:	n/a
37	chr4:26321873-26321923	AoSMC	blood vessel:	n/a
38	chr4:26321873-26321923	HIPEpiC	eye:	n/a
39	chr4:26321873-26321923	HRCEpiC	kidney:	n/a
40	chr4:26321873-26321923	HUVEC	blood vessel:	n/a
41	chr4:26321873-26321923	AG10803	skin:	n/a
42	chr4:26321873-26321923	SK-N-MC	brain:	n/a
43	chr4:26321873-26321923	Jurkat	blood:	n/a
44	chr4:26321873-26321923	HAEpiC	amniotic membrane:	n/a
45	chr4:26321873-26321923	AG04450	lung:	fetal
46	chr4:26321873-26321923	Hepatocyte	liver:	n/a
47	chr4:26321873-26321923	HCF	heart:	n/a
48	chr4:26321873-26321923	MCF-7	breast:	n/a
49	chr4:26321873-26321923	HPAEpiC	pulmonary alveolar:	n/a
50	chr4:26321873-26321923	HCM	heart:	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
RBPJ	CpG island
ENSG00000273010	Chromatin interaction
ENSG00000053900	Chromatin interaction
ENSG00000168214	Chromatin interaction
ENSG00000250317	Chromatin interaction
ENSG00000111011	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10008046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10009355	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10517097	0.84[TSI][hapmap]
rs12651502	0.85[CEU][hapmap]
rs2077777	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs34295457	0.81[EUR][1000 genomes]
rs56762644	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60730169	0.83[EUR][1000 genomes]
rs6448449	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6826838	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837108	0.87[ASN][1000 genomes]
rs6844691	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6847065	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs7657866	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680738	0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3822223	SEL1L3	cis	cerebellum	SCAN

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	chr4:26320400-26324200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:26320400-26324200	Active TSS	Fetal Intestine Large	intestine
14	chr4:26320400-26324400	Active TSS	HSMM	muscle
15	chr4:26320400-26324600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:26320400-26324600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr4:26320400-26324600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:26320400-26324600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:26320400-26324800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr4:26320400-26324800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:26320400-26325400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:26320400-26325400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:26320400-26326000	Active TSS	Fetal Brain Female	brain
24	chr4:26320600-26322200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:26320600-26323000	Active TSS	Brain Germinal Matrix	brain
26	chr4:26320600-26323200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:26320600-26323200	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr4:26320600-26323200	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr4:26320600-26323200	Active TSS	Thymus	Thymus
30	chr4:26320600-26323400	Active TSS	Brain Hippocampus Middle	brain
31	chr4:26320600-26323400	Active TSS	Right Ventricle	heart
32	chr4:26320600-26323600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:26320600-26323600	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr4:26320600-26323600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:26320600-26323600	Active TSS	Brain Cingulate Gyrus	brain
36	chr4:26320600-26323600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:26320600-26323600	Active TSS	Esophagus	oesophagus
38	chr4:26320600-26323600	Active TSS	Lung	lung
39	chr4:26320600-26323600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr4:26320600-26323600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr4:26320600-26323800	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr4:26320600-26323800	Active TSS	Brain Substantia Nigra	brain
43	chr4:26320600-26323800	Active TSS	Colon Smooth Muscle	Colon
44	chr4:26320600-26323800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr4:26320600-26323800	Active TSS	Fetal Intestine Small	intestine
46	chr4:26320600-26323800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr4:26320600-26323800	Active TSS	Small Intestine	intestine
48	chr4:26320600-26323800	Active TSS	NHEK	skin
49	chr4:26320600-26324000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:26320600-26324000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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