Variant report

Variant	rs3738176
Chromosome Location	chr1:220960240-220960241
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	chr1:220960237-220960301	Hela-S3	cervix:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
2	CTCF	chr1:220960178-220960319	Fibrobl	skin:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
3	CTCF	chr1:220960193-220960345	GM12892	blood:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
4	ZBTB7A	chr1:220960006-220960338	HepG2	liver:	n/a	n/a
5	CTCF	chr1:220960187-220960359	ProgFib	skin:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
6	MAX	chr1:220959764-220960971	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:220959533-220961147	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr1:220960191-220960349	LNCaP	prostate:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
9	MAZ	chr1:220959720-220961010	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr1:220960140-220960290	HA-sp	spinal cord:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
11	POLR2A	chr1:220959957-220960363	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr1:220960076-220960622	H1-hESC	embryonic stem cell:	n/a	chr1:220960128-220960137 chr1:220960582-220960593 chr1:220960125-220960134
13	POLR2A	chr1:220959900-220960467	HCT-116	colon:	n/a	n/a
14	HEY1	chr1:220959459-220960459	HepG2	liver:	n/a	n/a
15	CTCF	chr1:220960220-220960370	WERI-Rb-1	eye:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
16	HA-E2F1	chr1:220959917-220960915	Hela-S3	cervix:	n/a	chr1:220960125-220960134 chr1:220960572-220960581 chr1:220960574-220960583 chr1:220960156-220960165 chr1:220960776-220960790
17	POLR2A	chr1:220959907-220960432	HepG2	liver:	n/a	n/a
18	CTCF	chr1:220960180-220960330	GM12875	blood:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
19	CTCF	chr1:220960180-220960330	SK-N-SH_RA	brain:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
20	POLR2A	chr1:220959913-220960461	H1-neurons	neurons:	n/a	n/a
21	CTCF	chr1:220960180-220960330	HMF	breast:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
22	CTCF	chr1:220960188-220960347	Lung_OC	lung:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
23	EP300	chr1:220959961-220960408	T-47D	breast:	n/a	chr1:220960128-220960137 chr1:220960115-220960128
24	POLR2A	chr1:220959922-220960602	A549	lung:	n/a	n/a
25	CTCF	chr1:220960240-220960390	HUVEC	blood vessel:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
26	POLR2A	chr1:220960156-220960395	A549	lung:	n/a	n/a
27	MYC	chr1:220960023-220960884	H1-hESC	embryonic stem cell:	n/a	n/a
28	EP300	chr1:220960058-220960381	SK-N-SH_RA	brain:	n/a	chr1:220960128-220960137 chr1:220960115-220960128
29	HEY1	chr1:220959476-220961035	HepG2	liver:	n/a	n/a
30	CTCF	chr1:220960229-220960317	NHEK	skin:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
31	POLR2A	chr1:220959948-220960868	HCT-116	colon:	n/a	n/a
32	CTCF	chr1:220960209-220960295	H1-hESC	embryonic stem cell:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
33	CTCF	chr1:220960238-220960326	GM19238	blood:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
34	YY1	chr1:220960082-220960561	SK-N-SH_RA	brain:	n/a	chr1:220960128-220960137 chr1:220960125-220960134
35	MYC	chr1:220959942-220960965	NB4	blood:	n/a	n/a
36	MAX	chr1:220959476-220961100	Hela-S3	cervix:	n/a	n/a
37	NFIC	chr1:220959847-220960829	ECC-1	luminal epithelium:	n/a	chr1:220960192-220960209
38	EP300	chr1:220959842-220960442	HepG2	liver:	n/a	chr1:220960128-220960137 chr1:220960115-220960128
39	CTCF	chr1:220960200-220960350	GM12872	blood:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
40	POLR2A	chr1:220959941-220960422	HepG2	liver:	n/a	n/a
41	CTCF	chr1:220960174-220960377	MCF-7	breast:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
42	POLR2A	chr1:220958619-220961999	Hela-S3	cervix:	n/a	n/a
43	YY1	chr1:220960108-220960363	HCT-116	colon:	n/a	chr1:220960128-220960137 chr1:220960125-220960134
44	YY1	chr1:220959907-220960474	ECC-1	luminal epithelium:	n/a	chr1:220960128-220960137 chr1:220960125-220960134
45	POLR2A	chr1:220959565-220961053	HepG2	liver:	n/a	n/a
46	NFYB	chr1:220959937-220960282	Hela-S3	cervix:	n/a	chr1:220960152-220960167 chr1:220960156-220960168 chr1:220960152-220960167 chr1:220960154-220960169 chr1:220960153-220960167
47	REST	chr1:220959665-220960463	H1-neurons	neurons:	n/a	chr1:220960111-220960124
48	POLR2A	chr1:220959887-220960394	HepG2	liver:	n/a	n/a
49	CTCF	chr1:220960180-220960330	AG04449	skin:	n/a	chr1:220960262-220960275 chr1:220960260-220960278 chr1:220960261-220960277
50	SP1	chr1:220959898-220960385	HepG2	liver:	n/a	chr1:220960126-220960138 chr1:220960126-220960138 chr1:220960145-220960166

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:220960199-220960249	NB4	blood:	n/a
2	chr1:220960199-220960249	HRCEpiC	kidney:	n/a
3	chr1:220960199-220960249	HCF	heart:	n/a
4	chr1:220960199-220960249	GM12892	blood:	n/a
5	chr1:220960199-220960249	T-47D	breast:	n/a
6	chr1:220960199-220960249	ProgFib	skin:	n/a
7	chr1:220960199-220960249	U87	brain:	n/a
8	chr1:220960199-220960249	HEEpiC	esophagus:	n/a
9	chr1:220960199-220960249	SKMC	muscle:	n/a
10	chr1:220960199-220960249	K562	blood:	n/a
11	chr1:220960199-220960249	MCF10A-Er-Src	breast:	n/a
12	chr1:220960199-220960249	SAEC	small airway:	n/a
13	chr1:220960199-220960249	HRE	kidney:	n/a
14	chr1:220960199-220960249	NH-A	brain:	n/a
15	chr1:220960199-220960249	PrEC	prostate:	n/a
16	chr1:220960199-220960249	Caco-2	colon:	n/a
17	chr1:220960199-220960249	AG10803	skin:	n/a
18	chr1:220960199-220960249	CMK	blood:	n/a
19	chr1:220960199-220960249	NT2-D1	testis:	n/a
20	chr1:220960199-220960249	HCM	heart:	n/a
21	chr1:220960199-220960249	HCT-116	colon:	n/a
22	chr1:220960199-220960249	HUVEC	blood vessel:	n/a
23	chr1:220960199-220960249	GM19239	blood:	n/a
24	chr1:220960199-220960249	GM06990	blood:	n/a
25	chr1:220960199-220960249	IMR90	lung:	fetal
26	chr1:220960199-220960249	SK-N-MC	brain:	n/a
27	chr1:220960199-220960249	HCPEpiC	choroid plexus:	n/a
28	chr1:220960199-220960249	H1-hESC	embryonic stem cell:	embryo
29	chr1:220960199-220960249	AG09319	gingival:	n/a
30	chr1:220960199-220960249	PFSK-1	brain:	n/a
31	chr1:220960199-220960249	A549	lung:	n/a
32	chr1:220960199-220960249	NHBE	bronchial:	n/a
33	chr1:220960199-220960249	HNPCEpiC	eye:	n/a
34	chr1:220960199-220960249	SK-N-SH	brain:	n/a
35	chr1:220960199-220960249	HepG2	liver:	n/a
36	chr1:220960199-220960249	RPTEC	kidney:	n/a
37	chr1:220960199-220960249	HPAEpiC	pulmonary alveolar:	n/a
38	chr1:220960199-220960249	HL-60	blood:	n/a
39	chr1:220960199-220960249	Hela-S3	cervix:	n/a
40	chr1:220960199-220960249	PANC-1	pancreas:	n/a
41	chr1:220960199-220960249	BE2_C	brain:	n/a
42	chr1:220960199-220960249	GM12878	blood:	n/a
43	chr1:220960199-220960249	HMEC	breast:	n/a
44	chr1:220960199-220960249	ECC-1	luminal epithelium:	n/a
45	chr1:220960199-220960249	AG09309	skin:	n/a
46	chr1:220960199-220960249	AG04450	lung:	fetal
47	chr1:220960199-220960249	SK-N-SH_RA	brain:	n/a
48	chr1:220960199-220960249	ovcar-3	ovarian:	n/a
49	chr1:220960199-220960249	LNCaP	prostate:	n/a
50	chr1:220960199-220960249	HRPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220956529..220963831-chr1:220968712..220974793,12	MCF-7	breast:
2	chr1:220920087..220922800-chr1:220958239..220960991,2	MCF-7	breast:
3	chr1:220932972..220935057-chr1:220960206..220962159,2	MCF-7	breast:
4	chr1:220958915..220961807-chr1:220964103..220968214,4	MCF-7	breast:
5	chr1:220958940..220961119-chr1:220964763..220966587,2	MCF-7	breast:

Variant related genes	Relation type
MARC1	TF binding region
MARC1	CpG island
ENSG00000117791	Chromatin interaction
ENSG00000186205	Chromatin interaction

rs_ID	r²[population]
rs17008595	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17008643	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279636	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279637	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806327	0.95[ASN][1000 genomes]
rs72472382	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220939000-220960400	Weak transcription	Small Intestine	intestine
2	chr1:220959000-220962000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr1:220959200-220962600	Enhancers	Fetal Brain Male	brain
4	chr1:220959400-220960400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr1:220959400-220960600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:220959400-220960800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:220959400-220960800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr1:220959400-220961000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:220959400-220961000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr1:220959400-220961000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:220959400-220961000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:220959400-220961000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr1:220959400-220961000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:220959400-220961200	Active TSS	Brain Anterior Caudate	brain
15	chr1:220959400-220961400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:220959400-220961800	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:220959600-220960600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:220959600-220960600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:220959600-220960800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:220959600-220960800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:220959600-220960800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:220959600-220960800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:220959600-220960800	Active TSS	Psoas Muscle	Psoas
24	chr1:220959600-220960800	Active TSS	A549	lung
25	chr1:220959600-220960800	Active TSS	HSMM	muscle
26	chr1:220959600-220961000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr1:220959600-220961000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:220959600-220961000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:220959600-220961000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:220959600-220961000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:220959600-220961000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:220959600-220961000	Active TSS	Aorta	Aorta
33	chr1:220959600-220961000	Flanking Active TSS	Ovary	ovary
34	chr1:220959600-220961200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:220959600-220961200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:220959600-220961200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:220959600-220961200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr1:220959600-220961400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr1:220959600-220961400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:220959600-220961400	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:220959600-220961400	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr1:220959600-220961400	Active TSS	Brain Angular Gyrus	brain
43	chr1:220959600-220961400	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr1:220959600-220961600	Active TSS	HepG2	liver
45	chr1:220959600-220961800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:220959800-220960600	Active TSS	Fetal Lung	lung
47	chr1:220959800-220960600	Active TSS	Left Ventricle	heart
48	chr1:220959800-220960600	Active TSS	HSMMtube	muscle
49	chr1:220959800-220960600	Active TSS	NH-A	brain
50	chr1:220959800-220960800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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