Variant report

Variant	rs4468169
Chromosome Location	chr1:222628717-222628718
allele	C/T
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	CTCF	chr1:222628680-222628830	HCM	heart:	n/a	n/a
2	CTCF	chr1:222628600-222628750	NHEK	skin:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
3	CTCF	chr1:222628580-222628730	HCFaa	heart:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
4	CHD2	chr1:222628495-222628826	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:222628339-222629281	IMR90	lung:	n/a	chr1:222628638-222628659 chr1:222628945-222628954 chr1:222628643-222628661 chr1:222628644-222628660
6	MYC	chr1:222628517-222629059	H1-hESC	embryonic stem cell:	n/a	chr1:222628935-222628944 chr1:222628996-222629005
7	CTCF	chr1:222628600-222628750	GM12864	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
8	CTCF	chr1:222628526-222628799	ProgFib	skin:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
9	RAD21	chr1:222628098-222629076	SK-N-SH_RA	brain:	n/a	chr1:222628641-222628660
10	CTCF	chr1:222628620-222628770	HBMEC	blood vessel:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
11	CEBPB	chr1:222628523-222629133	H1-hESC	embryonic stem cell:	n/a	chr1:222628996-222629007
12	MXI1	chr1:222628519-222628773	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr1:222628504-222628813	GM12891	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
14	CTCF	chr1:222628580-222628730	GM12865	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
15	CTCF	chr1:222628580-222628730	WI-38	lung:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
16	FOS	chr1:222628567-222629115	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr1:222628512-222628803	LNCaP	prostate:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
18	CTCF	chr1:222628620-222628770	GM12871	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
19	CTCF	chr1:222628600-222628750	SK-N-SH_RA	brain:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
20	CTCF	chr1:222628431-222628770	K562	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
21	CTCF	chr1:222628472-222628770	HepG2	liver:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
22	CTCF	chr1:222628512-222628756	SK-N-SH_RA	brain:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
23	CTCF	chr1:222628502-222628813	NHEK	skin:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
24	CBX3	chr1:222628458-222629273	K562	blood:	n/a	n/a
25	RAD21	chr1:222628390-222628820	GM12878	blood:	n/a	chr1:222628641-222628660
26	CTCF	chr1:222628503-222628803	LNCaP	prostate:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
27	CEBPB	chr1:222628448-222629296	K562	blood:	n/a	chr1:222628996-222629007
28	CTCF	chr1:222628580-222628730	GM12873	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
29	CTCF	chr1:222628620-222628770	GM12874	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
30	CTCF	chr1:222628600-222628750	Caco-2	colon:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
31	JUN	chr1:222627968-222629964	K562	blood:	n/a	chr1:222628911-222628924 chr1:222628932-222628945
32	RAD21	chr1:222628386-222628907	ECC-1	luminal epithelium:	n/a	chr1:222628641-222628660
33	RAD21	chr1:222628411-222628839	HepG2	liver:	n/a	chr1:222628641-222628660
34	CTCF	chr1:222628600-222628750	AoAF	blood vessel:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
35	BRCA1	chr1:222628499-222629155	Hela-S3	cervix:	n/a	n/a
36	JUND	chr1:222628521-222629115	HepG2	liver:	n/a	n/a
37	CTCF	chr1:222628347-222628954	K562	blood:	n/a	chr1:222628638-222628659 chr1:222628945-222628954 chr1:222628643-222628661 chr1:222628644-222628660
38	CTCF	chr1:222628580-222628730	WERI-Rb-1	eye:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
39	EP300	chr1:222628469-222629259	K562	blood:	n/a	chr1:222628993-222629007 chr1:222628932-222628946
40	CTCF	chr1:222628500-222628811	A549	lung:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
41	CTCF	chr1:222628498-222628819	K562	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
42	MAFK	chr1:222628500-222628891	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr1:222628580-222628730	HMF	breast:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
44	ZNF143	chr1:222628505-222628965	H1-hESC	embryonic stem cell:	n/a	n/a
45	SMC3	chr1:222628302-222629181	Hela-S3	cervix:	n/a	chr1:222628645-222628659
46	SMC3	chr1:222628472-222629055	HepG2	liver:	n/a	chr1:222628645-222628659
47	CTCF	chr1:222628600-222628750	HCM	heart:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
48	CTCF	chr1:222628506-222628811	GM19239	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660
49	MYC	chr1:222628632-222628740	K562	blood:	n/a	n/a
50	CTCF	chr1:222628532-222628793	GM10248	blood:	n/a	chr1:222628638-222628659 chr1:222628643-222628661 chr1:222628644-222628660

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:222628702-222628752	HAEpiC	amniotic membrane:	n/a
2	chr1:222628702-222628752	HRCEpiC	kidney:	n/a
3	chr1:222628702-222628752	HIPEpiC	eye:	n/a
4	chr1:222628702-222628752	AG04450	lung:	fetal
5	chr1:222628702-222628752	LNCaP	prostate:	n/a
6	chr1:222628702-222628752	MCF10A-Er-Src	breast:	n/a
7	chr1:222628702-222628752	SK-N-SH_RA	brain:	n/a
8	chr1:222628702-222628752	GM19239	blood:	n/a
9	chr1:222628702-222628752	HUVEC	blood vessel:	n/a
10	chr1:222628702-222628752	AG09319	gingival:	n/a
11	chr1:222628702-222628752	HepG2	liver:	n/a
12	chr1:222628702-222628752	CMK	blood:	n/a
13	chr1:222628702-222628752	SKMC	muscle:	n/a
14	chr1:222628702-222628752	NHBE	bronchial:	n/a
15	chr1:222628702-222628752	HEEpiC	esophagus:	n/a
16	chr1:222628702-222628752	HNPCEpiC	eye:	n/a
17	chr1:222628702-222628752	HCPEpiC	choroid plexus:	n/a
18	chr1:222628702-222628752	PrEC	prostate:	n/a
19	chr1:222628702-222628752	BJ	skin:	n/a
20	chr1:222628702-222628752	T-47D	breast:	n/a
21	chr1:222628702-222628752	AoSMC	blood vessel:	n/a
22	chr1:222628702-222628752	A549	lung:	n/a
23	chr1:222628702-222628752	HCT-116	colon:	n/a
24	chr1:222628702-222628752	HMEC	breast:	n/a
25	chr1:222628702-222628752	PANC-1	pancreas:	n/a
26	chr1:222628702-222628752	IMR90	lung:	fetal
27	chr1:222628702-222628752	Caco-2	colon:	n/a
28	chr1:222628702-222628752	SAEC	small airway:	n/a
29	chr1:222628702-222628752	Hela-S3	cervix:	n/a
30	chr1:222628702-222628752	SK-N-MC	brain:	n/a
31	chr1:222628702-222628752	H1-hESC	embryonic stem cell:	embryo
32	chr1:222628702-222628752	Jurkat	blood:	n/a
33	chr1:222628702-222628752	NH-A	brain:	n/a
34	chr1:222628702-222628752	GM12892	blood:	n/a
35	chr1:222628702-222628752	AG09309	skin:	n/a
36	chr1:222628702-222628752	BE2_C	brain:	n/a
37	chr1:222628702-222628752	GM06990	blood:	n/a
38	chr1:222628702-222628752	HL-60	blood:	n/a
39	chr1:222628702-222628752	Hepatocyte	liver:	n/a
40	chr1:222628702-222628752	U87	brain:	n/a
41	chr1:222628702-222628752	HRPEpiC	eye:	n/a
42	chr1:222628702-222628752	GM12891	blood:	n/a
43	chr1:222628702-222628752	HPAEpiC	pulmonary alveolar:	n/a
44	chr1:222628702-222628752	ovcar-3	ovarian:	n/a
45	chr1:222628702-222628752	HRE	kidney:	n/a
46	chr1:222628702-222628752	SK-N-SH	brain:	n/a
47	chr1:222628702-222628752	AG04449	skin:	fetal
48	chr1:222628702-222628752	PFSK-1	brain:	n/a
49	chr1:222628702-222628752	NT2-D1	testis:	n/a
50	chr1:222628702-222628752	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:222628680..222632014-chr1:222636093..222640238,5	K562	blood:
2	chr1:222297313..222298602-chr1:222628186..222629290,6	MCF-7	breast:
3	chr1:222628658..222629520-chr1:222638274..222638881,2	K562	blood:
4	chr1:221651337..221652127-chr1:222628247..222629064,2	MCF-7	breast:
5	chr1:222297861..222298606-chr1:222628253..222629047,3	MCF-7	breast:
6	chr1:222268651..222270200-chr1:222628597..222629348,4	K562	blood:

Variant related genes	Relation type
ENSG00000226643	TF binding region
ENSG00000226643	CpG island

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4573528	0.82[AFR][1000 genomes]
rs73120940	1.00[EUR][1000 genomes]
rs74148116	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222626800-222629000	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr1:222627400-222629000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:222627600-222629000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr1:222627600-222629000	Enhancers	Fetal Lung	lung
5	chr1:222627600-222629000	Enhancers	Fetal Stomach	stomach
6	chr1:222627600-222629400	Enhancers	Fetal Muscle Leg	muscle
7	chr1:222627600-222629600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:222627800-222628800	Enhancers	Primary T cells from cord blood	blood
9	chr1:222627800-222629000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:222628000-222628800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:222628000-222628800	Enhancers	Pancreas	Pancrea
12	chr1:222628000-222629000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:222628000-222629000	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:222628000-222629000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:222628000-222629000	Enhancers	Colon Smooth Muscle	Colon
16	chr1:222628000-222629000	Enhancers	Fetal Heart	heart
17	chr1:222628000-222629000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr1:222628000-222629000	Flanking Active TSS	HMEC	breast
19	chr1:222628000-222629200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:222628000-222629200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:222628200-222628800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:222628200-222628800	Enhancers	Ovary	ovary
23	chr1:222628200-222629000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:222628200-222629000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:222628200-222629000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:222628200-222629000	Enhancers	Fetal Thymus	thymus
27	chr1:222628200-222629000	Flanking Active TSS	NH-A	brain
28	chr1:222628200-222629000	Flanking Active TSS	NHEK	skin
29	chr1:222628200-222629200	Flanking Active TSS	Osteobl	bone
30	chr1:222628400-222628800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:222628400-222628800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:222628400-222628800	Active TSS	Primary B cells from cord blood	blood
33	chr1:222628400-222628800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:222628400-222628800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:222628400-222629000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:222628400-222629000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:222628400-222629000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:222628400-222629000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:222628400-222629000	Enhancers	Fetal Intestine Small	intestine
40	chr1:222628400-222629000	Enhancers	Placenta	Placenta
41	chr1:222628400-222629000	Active TSS	Psoas Muscle	Psoas
42	chr1:222628400-222629000	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:222628400-222629000	Enhancers	Dnd41	blood
44	chr1:222628400-222629000	Active TSS	NHDF-Ad	bronchial
45	chr1:222628600-222628800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:222628600-222629000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:222628600-222629000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:222628600-222629000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:222628600-222629000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr1:222628600-222629000	Active TSS	Primary hematopoietic stem cells	blood

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