Variant report

Variant	rs4570386
Chromosome Location	chr1:226270779-226270780
allele	A/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	CTCF	chr1:226270734-226270794	GM10266	blood:	n/a	chr1:226270755-226270773
2	CTCF	chr1:226270700-226270850	HCPEpiC	choroid plexus:	n/a	chr1:226270755-226270773
3	MYC	chr1:226270682-226270871	MCF-7	breast:	n/a	n/a
4	UBTF	chr1:226270692-226271519	K562	blood:	n/a	n/a
5	MAX	chr1:226270487-226271728	HUVEC	blood vessel:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
6	HCFC1	chr1:226270389-226271769	Hela-S3	cervix:	n/a	n/a
7	SIN3AK20	chr1:226270589-226271034	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr1:226270714-226271767	HepG2	liver:	n/a	n/a
9	E2F6	chr1:226270627-226271648	K562	blood:	n/a	chr1:226271513-226271523 chr1:226271481-226271493
10	SMARCB1	chr1:226270565-226271883	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr1:226270660-226270810	GM12871	blood:	n/a	chr1:226270755-226270773
12	SIN3AK20	chr1:226270677-226271611	SK-N-SH	brain:	n/a	n/a
13	MAX	chr1:226270531-226271932	MCF-7	breast:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
14	CTCF	chr1:226270640-226270790	HBMEC	blood vessel:	n/a	chr1:226270755-226270773
15	MAX	chr1:226270454-226271734	K562	blood:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
16	THAP1	chr1:226270675-226271598	K562	blood:	n/a	n/a
17	MAX	chr1:226270511-226271939	A549	lung:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
18	CBX3	chr1:226270300-226271707	K562	blood:	n/a	n/a
19	MXI1	chr1:226270157-226272016	SK-N-SH	brain:	n/a	n/a
20	MAX	chr1:226270650-226271700	A549	lung:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
21	MAX	chr1:226270430-226271996	HCT-116	colon:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
22	USF1	chr1:226270556-226271867	SK-N-SH	brain:	n/a	chr1:226271222-226271243 chr1:226271228-226271237 chr1:226271226-226271239 chr1:226271555-226271571 chr1:226271227-226271236 chr1:226271228-226271237 chr1:226271227-226271238 chr1:226271229-226271238
23	STAT1	chr1:226270673-226270873	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:226270684-226271507	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:226270599-226271460	Hela-S3	cervix:	n/a	n/a
26	RCOR1	chr1:226270664-226271351	Hela-S3	cervix:	n/a	n/a
27	MAX	chr1:226270582-226271730	Hela-S3	cervix:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
28	E2F6	chr1:226270595-226271782	K562	blood:	n/a	chr1:226271513-226271523 chr1:226271481-226271493
29	CTCF	chr1:226270720-226270870	SK-N-SH_RA	brain:	n/a	chr1:226270755-226270773
30	CTCF	chr1:226270718-226270787	Hela-S3	cervix:	n/a	chr1:226270755-226270773
31	ELF1	chr1:226270626-226271014	K562	blood:	n/a	chr1:226270811-226270824
32	POLR2A	chr1:226270462-226271540	Hela-S3	cervix:	n/a	n/a
33	GABPA	chr1:226270551-226271038	A549	lung:	n/a	n/a
34	CTCF	chr1:226270640-226270790	AG09319	gingival:	n/a	chr1:226270755-226270773
35	CTCF	chr1:226270660-226270810	GM12870	blood:	n/a	chr1:226270755-226270773
36	POLR2A	chr1:226270720-226271512	K562	blood:	n/a	n/a
37	YY1	chr1:226270612-226271633	K562	blood:	n/a	chr1:226271127-226271138 chr1:226270754-226270774 chr1:226270986-226270997 chr1:226270755-226270774 chr1:226270763-226270771
38	CTCF	chr1:226270725-226270781	MCF-7	breast:	n/a	chr1:226270755-226270773
39	POLR2A	chr1:226270762-226271488	GM18505	blood:	n/a	n/a
40	POLR2A	chr1:226270583-226271713	Raji	blood:	n/a	n/a
41	SP1	chr1:226270560-226271856	A549	lung:	n/a	chr1:226270577-226270591 chr1:226271055-226271064 chr1:226270987-226271001 chr1:226271273-226271283 chr1:226270581-226270590 chr1:226270979-226270991 chr1:226271254-226271266 chr1:226271255-226271265 chr1:226270981-226270990 chr1:226271273-226271283 chr1:226270988-226270997 chr1:226270986-226270998 chr1:226271255-226271265 chr1:226270980-226270994 chr1:226270580-226270592 chr1:226271254-226271266 chr1:226270874-226270884 chr1:226270986-226270998
42	POLR2A	chr1:226270618-226271765	ECC-1	luminal epithelium:	n/a	n/a
43	CHD2	chr1:226270593-226271450	Hela-S3	cervix:	n/a	chr1:226270981-226270991 chr1:226270988-226270998
44	GABPA	chr1:226270524-226271609	K562	blood:	n/a	n/a
45	TAF1	chr1:226270652-226270899	K562	blood:	n/a	n/a
46	E2F6	chr1:226270565-226271754	H1-hESC	embryonic stem cell:	n/a	chr1:226271513-226271523 chr1:226271481-226271493
47	RFX5	chr1:226270713-226271471	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr1:226270593-226271691	A549	lung:	n/a	n/a
49	MAX	chr1:226270524-226271955	HepG2	liver:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
50	CTCF	chr1:226270684-226270814	MCF-7	breast:	n/a	chr1:226270755-226270773

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:226270741-226270791	NHDF-neo	bronchial:	n/a
2	chr1:226270741-226270791	AoSMC	blood vessel:	n/a
3	chr1:226270741-226270791	HCT-116	colon:	n/a
4	chr1:226270741-226270791	HPAEpiC	pulmonary alveolar:	n/a
5	chr1:226270741-226270791	AG04449	skin:	fetal
6	chr1:226270741-226270791	PrEC	prostate:	n/a
7	chr1:226270741-226270791	HepG2	liver:	n/a
8	chr1:226270741-226270791	HL-60	blood:	n/a
9	chr1:226270741-226270791	PANC-1	pancreas:	n/a
10	chr1:226270741-226270791	U87	brain:	n/a
11	chr1:226270741-226270791	GM19239	blood:	n/a
12	chr1:226270741-226270791	H1-hESC	embryonic stem cell:	embryo
13	chr1:226270741-226270791	GM06990	blood:	n/a
14	chr1:226270741-226270791	BJ	skin:	n/a
15	chr1:226270741-226270791	ProgFib	skin:	n/a
16	chr1:226270741-226270791	HRE	kidney:	n/a
17	chr1:226270741-226270791	MCF-7	breast:	n/a
18	chr1:226270741-226270791	AG10803	skin:	n/a
19	chr1:226270741-226270791	LNCaP	prostate:	n/a
20	chr1:226270741-226270791	HMEC	breast:	n/a
21	chr1:226270741-226270791	RPTEC	kidney:	n/a
22	chr1:226270741-226270791	Jurkat	blood:	n/a
23	chr1:226270741-226270791	HIPEpiC	eye:	n/a
24	chr1:226270741-226270791	HCF	heart:	n/a
25	chr1:226270741-226270791	MCF10A-Er-Src	breast:	n/a
26	chr1:226270741-226270791	Caco-2	colon:	n/a
27	chr1:226270741-226270791	K562	blood:	n/a
28	chr1:226270741-226270791	ovcar-3	ovarian:	n/a
29	chr1:226270741-226270791	CMK	blood:	n/a
30	chr1:226270741-226270791	AG04450	lung:	fetal
31	chr1:226270741-226270791	ECC-1	luminal epithelium:	n/a
32	chr1:226270741-226270791	HAEpiC	amniotic membrane:	n/a
33	chr1:226270741-226270791	Hepatocyte	liver:	n/a
34	chr1:226270741-226270791	PFSK-1	brain:	n/a
35	chr1:226270741-226270791	AG09309	skin:	n/a
36	chr1:226270741-226270791	HCM	heart:	n/a
37	chr1:226270741-226270791	GM12878	blood:	n/a
38	chr1:226270741-226270791	A549	lung:	n/a
39	chr1:226270741-226270791	HEEpiC	esophagus:	n/a
40	chr1:226270741-226270791	IMR90	lung:	fetal
41	chr1:226270741-226270791	SAEC	small airway:	n/a
42	chr1:226270741-226270791	NHBE	bronchial:	n/a
43	chr1:226270741-226270791	SK-N-SH	brain:	n/a
44	chr1:226270741-226270791	SK-N-MC	brain:	n/a
45	chr1:226270741-226270791	Hela-S3	cervix:	n/a
46	chr1:226270741-226270791	T-47D	breast:	n/a
47	chr1:226270741-226270791	BE2_C	brain:	n/a
48	chr1:226270741-226270791	AG09319	gingival:	n/a
49	chr1:226270741-226270791	HEK293	kidney:	embryo
50	chr1:226270741-226270791	NH-A	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226245847..226247629-chr1:226268989..226271132,2	MCF-7	breast:
2	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
3	chr1:226248789..226253333-chr1:226269675..226273948,8	MCF-7	breast:
4	chr1:226270770..226272699-chr1:226374583..226377096,2	MCF-7	breast:
5	chr1:226269153..226271287-chr1:226280169..226282555,2	K562	blood:
6	chr1:226262247..226264355-chr1:226268888..226270936,2	MCF-7	breast:
7	chr1:226185497..226187877-chr1:226269946..226272750,2	MCF-7	breast:
8	chr1:226270697..226271458-chr19:17402924..17403905,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000225518	TF binding region
ENSG00000225518	CpG island
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000223570	Chromatin interaction
ENSG00000130312	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10915928	0.81[ASN][1000 genomes]
rs10915933	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12123950	0.86[EUR][1000 genomes]
rs12131977	0.86[EUR][1000 genomes]
rs12138509	0.80[ASN][1000 genomes]
rs34374657	0.81[AFR][1000 genomes]
rs4592232	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226270200-226270800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
2	chr1:226270200-226271400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:226270400-226270800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
4	chr1:226270400-226270800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:226270400-226270800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:226270400-226270800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:226270400-226270800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr1:226270400-226270800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr1:226270400-226270800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
10	chr1:226270400-226270800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:226270400-226270800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:226270400-226270800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr1:226270400-226270800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr1:226270400-226270800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:226270400-226270800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr1:226270400-226270800	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr1:226270400-226270800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:226270400-226270800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:226270400-226270800	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr1:226270400-226270800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr1:226270400-226270800	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr1:226270400-226270800	Flanking Active TSS	Ovary	ovary
23	chr1:226270400-226270800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr1:226270400-226270800	Flanking Active TSS	Stomach Mucosa	stomach
25	chr1:226270400-226270800	Flanking Active TSS	A549	lung
26	chr1:226270400-226270800	Flanking Active TSS	GM12878-XiMat	blood
27	chr1:226270400-226270800	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr1:226270400-226270800	Flanking Active TSS	HSMM	muscle
29	chr1:226270400-226270800	Flanking Active TSS	K562	blood
30	chr1:226270400-226270800	Flanking Active TSS	NH-A	brain
31	chr1:226270400-226270800	Flanking Active TSS	NHEK	skin
32	chr1:226270400-226270800	Flanking Active TSS	NHLF	lung
33	chr1:226270400-226270800	Flanking Active TSS	Osteobl	bone
34	chr1:226270400-226271000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:226270400-226271000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:226270400-226271000	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:226270400-226271000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr1:226270400-226271000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:226270400-226271000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr1:226270400-226271000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:226270400-226271000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:226270400-226271000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:226270400-226271000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:226270400-226271000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:226270400-226271000	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr1:226270400-226271000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr1:226270400-226271000	Flanking Active TSS	Fetal Brain Female	brain
48	chr1:226270400-226271000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr1:226270400-226271000	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr1:226270400-226271000	Flanking Bivalent TSS/Enh	Thymus	Thymus

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