Variant report

Variant	rs3748691
Chromosome Location	chr1:214776607-214776608
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	ZNF143	chr1:214776170-214776799	GM12878	blood:	n/a	n/a
2	REST	chr1:214775984-214776785	A549	lung:	n/a	n/a
3	HMGN3	chr1:214776209-214776903	K562	blood:	n/a	n/a
4	SIN3AK20	chr1:214776389-214776733	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr1:214776580-214776730	GM12875	blood:	n/a	n/a
6	YY1	chr1:214776416-214776671	K562	blood:	n/a	n/a
7	NFYB	chr1:214776183-214776735	Hela-S3	cervix:	n/a	chr1:214776476-214776491 chr1:214776497-214776512
8	SIN3AK20	chr1:214775919-214777017	HCT-116	colon:	n/a	n/a
9	CTCF	chr1:214776208-214776696	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:214775932-214777552	PANC-1	pancreas:	n/a	n/a
11	ATF1	chr1:214775849-214776633	K562	blood:	n/a	n/a
12	E2F4	chr1:214776137-214777114	K562	blood:	n/a	chr1:214776468-214776477 chr1:214776699-214776708 chr1:214776441-214776450 chr1:214776713-214776722
13	POLR2A	chr1:214776003-214776778	U87	brain:	n/a	n/a
14	MXI1	chr1:214775847-214776944	K562	blood:	n/a	n/a
15	KAP1	chr1:214776018-214776631	HEK293	kidney:	n/a	n/a
16	POLR2A	chr1:214776467-214776956	GM12878	blood:	n/a	n/a
17	TBP	chr1:214776015-214777465	K562	blood:	n/a	n/a
18	POLR2A	chr1:214776163-214776807	ProgFib	skin:	n/a	n/a
19	POLR2A	chr1:214776155-214776943	HCT-116	colon:	n/a	n/a
20	POLR2A	chr1:214776022-214777605	K562	blood:	n/a	n/a
21	SRF	chr1:214776064-214776711	ECC-1	luminal epithelium:	n/a	n/a
22	JUND	chr1:214776028-214777022	K562	blood:	n/a	chr1:214776716-214776725 chr1:214776443-214776452
23	SP1	chr1:214776120-214776714	HepG2	liver:	n/a	chr1:214776440-214776461 chr1:214776501-214776522
24	POLR2A	chr1:214776121-214777119	IMR90	lung:	n/a	n/a
25	E2F6	chr1:214776120-214776909	K562	blood:	n/a	chr1:214776468-214776477 chr1:214776699-214776708 chr1:214776441-214776450 chr1:214776713-214776722
26	NR2F2	chr1:214775886-214777467	K562	blood:	n/a	n/a
27	POLR2A	chr1:214776112-214776990	A549	lung:	n/a	n/a
28	FOXM1	chr1:214776072-214777128	SK-N-SH	brain:	n/a	n/a
29	MYC	chr1:214776086-214776923	Hela-S3	cervix:	n/a	chr1:214776343-214776352 chr1:214776723-214776732 chr1:214776341-214776354 chr1:214776343-214776352 chr1:214776341-214776354 chr1:214776344-214776353 chr1:214776342-214776353 chr1:214776814-214776824 chr1:214776339-214776354 chr1:214776344-214776351 chr1:214776342-214776352 chr1:214776341-214776354 chr1:214776341-214776354 chr1:214776341-214776351 chr1:214776343-214776353 chr1:214776342-214776353 chr1:214776343-214776353
30	ELF1	chr1:214776107-214776713	HepG2	liver:	n/a	n/a
31	MYC	chr1:214775873-214777626	K562	blood:	n/a	chr1:214776343-214776352 chr1:214776723-214776732 chr1:214776341-214776354 chr1:214776343-214776352 chr1:214776341-214776354 chr1:214776344-214776353 chr1:214776342-214776353 chr1:214776814-214776824 chr1:214776339-214776354 chr1:214776344-214776351 chr1:214776342-214776352 chr1:214776341-214776354 chr1:214776341-214776354 chr1:214775932-214775941 chr1:214776341-214776351 chr1:214776343-214776353 chr1:214776342-214776353 chr1:214776343-214776353
32	E2F4	chr1:214776019-214776903	GM12878	blood:	n/a	chr1:214776468-214776477 chr1:214776699-214776708 chr1:214776441-214776450 chr1:214776713-214776722
33	SIN3AK20	chr1:214776176-214776761	HepG2	liver:	n/a	n/a
34	USF1	chr1:214775932-214776927	HCT-116	colon:	n/a	n/a
35	CEBPD	chr1:214775926-214776784	K562	blood:	n/a	n/a
36	TAF1	chr1:214776119-214777007	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr1:214776438-214776749	SK-N-SH	brain:	n/a	n/a
38	SIN3AK20	chr1:214776100-214777103	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr1:214776103-214776806	HepG2	liver:	n/a	n/a
40	ELK1	chr1:214776108-214776630	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:214776199-214776960	Gliobla	brain:	n/a	n/a
42	UBTF	chr1:214776162-214777066	K562	blood:	n/a	n/a
43	PML	chr1:214775941-214776728	K562	blood:	n/a	n/a
44	POLR2A	chr1:214776471-214776715	HepG2	liver:	n/a	n/a
45	E2F6	chr1:214775861-214777026	K562	blood:	n/a	chr1:214776468-214776477 chr1:214776699-214776708 chr1:214776441-214776450 chr1:214776713-214776722
46	ELF1	chr1:214776171-214776833	K562	blood:	n/a	n/a
47	CTCF	chr1:214776460-214776610	GM12870	blood:	n/a	n/a
48	ELF1	chr1:214776112-214776698	GM12878	blood:	n/a	n/a
49	RCOR1	chr1:214776140-214776786	Hela-S3	cervix:	n/a	n/a
50	FOXA2	chr1:214776269-214776713	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:214774784..214777425-chr1:214779446..214783969,6	K562	blood:
2	chr1:214773497..214776791-chr1:214785798..214789572,5	K562	blood:
3	chr1:214452363..214455450-chr1:214775239..214777636,3	K562	blood:

Variant related genes	Relation type
CENPF	TF binding region
ENSG00000143499	Chromatin interaction
ENSG00000224584	Chromatin interaction
ENSG00000250536	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11801893	0.89[AMR][1000 genomes]
rs1511049	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1511050	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070065	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2666834	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2666839	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2807662	0.98[ASN][1000 genomes]
rs2809588	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748693	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57338227	0.82[AMR][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	nsv1004475	chr1:214763778-215013375	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv10993	chr1:214774207-214778763	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv1791911	chr1:214774278-214776936	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1005669	chr1:214774522-214994142	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr1:214775600-214776800	Active TSS	Stomach Smooth Muscle	stomach
2	chr1:214775600-214777000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:214775600-214777200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:214775600-214777400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:214775600-214777800	Active TSS	A549	lung
6	chr1:214775800-214776800	Active TSS	Primary B cells from cord blood	blood
7	chr1:214775800-214776800	Active TSS	Primary T cells from cord blood	blood
8	chr1:214775800-214776800	Active TSS	Primary T cells fromperipheralblood	blood
9	chr1:214775800-214776800	Active TSS	Brain Angular Gyrus	brain
10	chr1:214775800-214776800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:214775800-214776800	Active TSS	Brain Substantia Nigra	brain
12	chr1:214775800-214776800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr1:214775800-214776800	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:214775800-214777000	Active TSS	Brain Germinal Matrix	brain
15	chr1:214775800-214777000	Active TSS	Colon Smooth Muscle	Colon
16	chr1:214775800-214777000	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr1:214775800-214777000	Active TSS	Fetal Muscle Leg	muscle
18	chr1:214775800-214777000	Active TSS	Fetal Stomach	stomach
19	chr1:214775800-214777000	Active TSS	NHLF	lung
20	chr1:214775800-214777000	Active TSS	Osteobl	bone
21	chr1:214775800-214777200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:214775800-214777200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:214775800-214777200	Active TSS	Brain Anterior Caudate	brain
24	chr1:214775800-214777200	Active TSS	Brain Hippocampus Middle	brain
25	chr1:214775800-214777200	Active TSS	Fetal Brain Female	brain
26	chr1:214775800-214777200	Active TSS	Fetal Muscle Trunk	muscle
27	chr1:214775800-214777200	Active TSS	Ovary	ovary
28	chr1:214775800-214777200	Active TSS	Psoas Muscle	Psoas
29	chr1:214775800-214777200	Active TSS	Right Atrium	heart
30	chr1:214775800-214777200	Active TSS	NH-A	brain
31	chr1:214775800-214777400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:214775800-214777400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:214775800-214777400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:214775800-214777600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr1:214775800-214777600	Active TSS	HSMMtube	muscle
36	chr1:214775800-214777800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:214775800-214777800	Active TSS	Fetal Intestine Small	intestine
38	chr1:214775800-214777800	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr1:214775800-214777800	Active TSS	Rectal Smooth Muscle	rectum
40	chr1:214775800-214778000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:214775800-214778000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr1:214775800-214778000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:214775800-214778000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:214775800-214778000	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:214775800-214778200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:214775800-214778200	Active TSS	HSMM	muscle
47	chr1:214775800-214778600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:214775800-214778600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:214776000-214776800	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:214776000-214776800	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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