Variant report

Variant	rs72542443
Chromosome Location	chr1:169455199-169455200
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:596)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:596 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr1:169455083-169455501	A549	lung:	n/a	n/a
2	ETS1	chr1:169454689-169455506	K562	blood:	n/a	chr1:169455132-169455143
3	PML	chr1:169454817-169455676	MCF-7	breast:	n/a	n/a
4	TFAP2C	chr1:169454455-169455732	Hela-S3	cervix:	n/a	n/a
5	GTF2B	chr1:169454970-169455661	K562	blood:	n/a	n/a
6	USF1	chr1:169455105-169455454	A549	lung:	n/a	n/a
7	TBP	chr1:169454976-169455626	GM12878	blood:	n/a	n/a
8	CTCF	chr1:169455060-169455210	GM12864	blood:	n/a	n/a
9	CCNT2	chr1:169454604-169455681	K562	blood:	n/a	chr1:169455015-169455024
10	MXI1	chr1:169453845-169456810	SK-N-SH	brain:	n/a	n/a
11	CTCF	chr1:169455100-169455250	HPAF	blood vessel:	n/a	n/a
12	POLR2A	chr1:169454751-169455777	ProgFib	skin:	n/a	n/a
13	SP1	chr1:169454953-169455615	H1-hESC	embryonic stem cell:	n/a	chr1:169455014-169455026 chr1:169455015-169455024
14	GATA3	chr1:169454978-169455638	T-47D	breast:	n/a	n/a
15	SIN3AK20	chr1:169454997-169455555	HepG2	liver:	n/a	n/a
16	TAF1	chr1:169455055-169455605	PFSK-1	brain:	n/a	n/a
17	CTCF	chr1:169455080-169455230	GM12865	blood:	n/a	n/a
18	MYC	chr1:169454919-169455545	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOXA1	chr1:169455009-169455679	HepG2	liver:	n/a	n/a
20	PBX3	chr1:169454978-169455661	A549	lung:	n/a	n/a
21	CTCF	chr1:169455092-169455269	GM10266	blood:	n/a	n/a
22	CTCF	chr1:169455072-169455300	GM12892	blood:	n/a	n/a
23	CTCF	chr1:169455100-169455250	NHLF	lung:	n/a	n/a
24	CTCF	chr1:169455006-169455637	IMR90	lung:	n/a	n/a
25	CHD1	chr1:169454918-169455619	GM12878	blood:	n/a	chr1:169455009-169455019
26	CTCF	chr1:169455100-169455250	AG09319	gingival:	n/a	n/a
27	CTCF	chr1:169455175-169455206	GM13977	blood:	n/a	n/a
28	POLR2A	chr1:169454762-169455717	GM12878	blood:	n/a	n/a
29	CTCF	chr1:169455100-169455250	Hela-S3	cervix:	n/a	n/a
30	TBL1XR1	chr1:169454706-169455491	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:169454742-169455787	SK-N-MC	brain:	n/a	n/a
32	CREB1	chr1:169455063-169455613	ECC-1	luminal epithelium:	n/a	n/a
33	NR3C1	chr1:169454716-169455742	A549	lung:	n/a	chr1:169455115-169455132
34	TAF1	chr1:169454739-169455717	Hela-S3	cervix:	n/a	n/a
35	USF1	chr1:169455058-169455564	H1-hESC	embryonic stem cell:	n/a	n/a
36	MYC	chr1:169455092-169455541	K562	blood:	n/a	n/a
37	BRCA1	chr1:169454999-169456158	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr1:169454981-169455651	PFSK-1	brain:	n/a	n/a
39	USF2	chr1:169455082-169455585	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr1:169453879-169456142	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr1:169455097-169455265	NHEK	skin:	n/a	n/a
42	TAF1	chr1:169454493-169455849	ECC-1	luminal epithelium:	n/a	n/a
43	TAF1	chr1:169454974-169455641	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr1:169455049-169455538	HepG2	liver:	n/a	n/a
45	MYC	chr1:169454014-169456207	MCF10A-Er-Src	breast:	n/a	n/a
46	BCLAF1	chr1:169455128-169455685	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:169454469-169455761	MCF-7	breast:	n/a	n/a
48	IRF1	chr1:169455035-169455702	K562	blood:	n/a	n/a
49	CTCF	chr1:169454963-169455371	K562	blood:	n/a	n/a
50	POLR2A	chr1:169454437-169455995	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:169455176-169455226	GM06990	blood:	n/a
2	chr1:169455176-169455226	MCF10A-Er-Src	breast:	n/a
3	chr1:169455176-169455226	HCM	heart:	n/a
4	chr1:169455176-169455226	RPTEC	kidney:	n/a
5	chr1:169455176-169455226	Hepatocyte	liver:	n/a
6	chr1:169455176-169455226	HepG2	liver:	n/a
7	chr1:169455176-169455226	HRE	kidney:	n/a
8	chr1:169455176-169455226	CMK	blood:	n/a
9	chr1:169455176-169455226	U87	brain:	n/a
10	chr1:169455176-169455226	NHDF-neo	bronchial:	n/a
11	chr1:169455176-169455226	GM12891	blood:	n/a
12	chr1:169455176-169455226	Caco-2	colon:	n/a
13	chr1:169455176-169455226	HIPEpiC	eye:	n/a
14	chr1:169455176-169455226	NB4	blood:	n/a
15	chr1:169455176-169455226	LNCaP	prostate:	n/a
16	chr1:169455176-169455226	HL-60	blood:	n/a
17	chr1:169455176-169455226	ovcar-3	ovarian:	n/a
18	chr1:169455176-169455226	HRPEpiC	eye:	n/a
19	chr1:169455176-169455226	HNPCEpiC	eye:	n/a
20	chr1:169455176-169455226	ProgFib	skin:	n/a
21	chr1:169455176-169455226	NH-A	brain:	n/a
22	chr1:169455176-169455226	NHBE	bronchial:	n/a
23	chr1:169455176-169455226	T-47D	breast:	n/a
24	chr1:169455176-169455226	AG10803	skin:	n/a
25	chr1:169455176-169455226	PANC-1	pancreas:	n/a
26	chr1:169455176-169455226	K562	blood:	n/a
27	chr1:169455176-169455226	HCT-116	colon:	n/a
28	chr1:169455176-169455226	HAEpiC	amniotic membrane:	n/a
29	chr1:169455176-169455226	IMR90	lung:	fetal
30	chr1:169455176-169455226	HUVEC	blood vessel:	n/a
31	chr1:169455176-169455226	HCPEpiC	choroid plexus:	n/a
32	chr1:169455176-169455226	GM12878	blood:	n/a
33	chr1:169455176-169455226	SK-N-SH	brain:	n/a
34	chr1:169455176-169455226	H1-hESC	embryonic stem cell:	embryo
35	chr1:169455176-169455226	HCF	heart:	n/a
36	chr1:169455176-169455226	AG04449	skin:	fetal
37	chr1:169455176-169455226	Hela-S3	cervix:	n/a
38	chr1:169455176-169455226	AG04450	lung:	fetal
39	chr1:169455176-169455226	ECC-1	luminal epithelium:	n/a
40	chr1:169455176-169455226	SKMC	muscle:	n/a
41	chr1:169455176-169455226	BJ	skin:	n/a
42	chr1:169455176-169455226	Jurkat	blood:	n/a
43	chr1:169455176-169455226	PFSK-1	brain:	n/a
44	chr1:169455176-169455226	SAEC	small airway:	n/a
45	chr1:169455176-169455226	HEK293	kidney:	embryo
46	chr1:169455176-169455226	A549	lung:	n/a
47	chr1:169455176-169455226	AG09309	skin:	n/a
48	chr1:169455176-169455226	SK-N-MC	brain:	n/a
49	chr1:169455176-169455226	PrEC	prostate:	n/a
50	chr1:169455176-169455226	HEEpiC	esophagus:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169454840..169455424-chr3:156878085..156879028,2	Hela-S3	cervix:
4	chr1:16481268..16482180-chr1:169454924..169455428,2	Hela-S3	cervix:
5	chr1:169454738..169455424-chr1:228783655..228784433,2	Hela-S3	cervix:
6	chr1:169454285..169455235-chr2:20646608..20647266,2	Hela-S3	cervix:
7	chr1:169454576..169455277-chr16:2205028..2205838,2	Hela-S3	cervix:
8	chr1:169454698..169455429-chr15:64752786..64753721,2	Hela-S3	cervix:
9	chr1:16840029..16840801-chr1:169454808..169455627,2	HCT-116	colon:
10	chr1:169454789..169455681-chr12:54385187..54385687,2	Hela-S3	cervix:
11	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

No data

Variant related genes	Relation type
SLC19A2	TF binding region
ENSG00000213062	TF binding region
SLC19A2	CpG island
ENSG00000213062	CpG island
ENSG00000206652	Chromatin interaction
ENSG00000212237	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000198734	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000131653	Chromatin interaction
ENSG00000207924	Chromatin interaction
ENSG00000227959	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000180357	Chromatin interaction
ENSG00000000460	Chromatin interaction

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

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

rs_ID	r²[population]
rs2420370	0.86[AFR][1000 genomes]
rs4264045	0.86[AFR][1000 genomes]
rs970740	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr1:169448000-169457000	Active TSS	Right Ventricle	heart
2	chr1:169450000-169456000	Active TSS	Psoas Muscle	Psoas
3	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:169451800-169455400	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:169452200-169456200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:169452600-169455600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:169452600-169457000	Active TSS	Left Ventricle	heart
8	chr1:169452800-169455400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:169452800-169455600	Active TSS	HepG2	liver
10	chr1:169452800-169456000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:169452800-169456000	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:169452800-169456200	Active TSS	Ovary	ovary
13	chr1:169453200-169455800	Active TSS	Esophagus	oesophagus
14	chr1:169453200-169456000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:169453200-169456000	Active TSS	Placenta	Placenta
16	chr1:169453200-169456200	Active TSS	Pancreas	Pancrea
17	chr1:169453400-169455800	Active TSS	Fetal Stomach	stomach
18	chr1:169453400-169455800	Active TSS	Lung	lung
19	chr1:169453400-169456000	Active TSS	Colonic Mucosa	Colon
20	chr1:169453400-169456200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:169453400-169456600	Active TSS	Aorta	Aorta
22	chr1:169453600-169455800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:169453600-169456000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:169453600-169456200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:169453600-169457000	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr1:169453600-169457200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:169453800-169455600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:169453800-169455800	Active TSS	HSMM	muscle
29	chr1:169453800-169456000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr1:169453800-169456200	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:169453800-169456400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr1:169453800-169456400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:169454000-169455600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:169454000-169455800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:169454000-169456200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr1:169454000-169456200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:169454000-169456200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr1:169454200-169455600	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr1:169454200-169455600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:169454200-169455600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr1:169454200-169455600	Active TSS	Gastric	stomach
42	chr1:169454200-169455600	Active TSS	Small Intestine	intestine
43	chr1:169454200-169455800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:169454200-169455800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:169454200-169455800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:169454200-169455800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:169454200-169455800	Active TSS	Brain Germinal Matrix	brain
48	chr1:169454200-169455800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr1:169454200-169455800	Active TSS	Hela-S3	cervix
50	chr1:169454200-169456000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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