Variant report

Variant	rs3008652
Chromosome Location	chr1:222763249-222763250
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	POLR2A	chr1:222762884-222764007	GM15510	blood:	n/a	n/a
2	SIN3A	chr1:222762806-222763537	GM12878	blood:	n/a	n/a
3	GABPA	chr1:222762696-222764061	SK-N-SH	brain:	n/a	n/a
4	TAF1	chr1:222762998-222763528	K562	blood:	n/a	n/a
5	GABPA	chr1:222762931-222763613	Hela-S3	cervix:	n/a	n/a
6	NR2F2	chr1:222762837-222763552	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr1:222762584-222763738	HCT-116	colon:	n/a	n/a
8	SIN3AK20	chr1:222762787-222763583	PFSK-1	brain:	n/a	n/a
9	ELF1	chr1:222762973-222763512	HepG2	liver:	n/a	n/a
10	SRF	chr1:222763058-222763249	GM12878	blood:	n/a	n/a
11	ZKSCAN1	chr1:222762898-222763420	Hela-S3	cervix:	n/a	n/a
12	YY1	chr1:222763075-222763397	K562	blood:	n/a	n/a
13	ELF1	chr1:222762935-222763394	K562	blood:	n/a	n/a
14	FOS	chr1:222762973-222763448	MCF10A-Er-Src	breast:	n/a	n/a
15	ETS1	chr1:222762958-222763422	GM12878	blood:	n/a	n/a
16	YY1	chr1:222763025-222763566	GM12878	blood:	n/a	n/a
17	TAF1	chr1:222762962-222763561	K562	blood:	n/a	n/a
18	RFX5	chr1:222763196-222763608	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:222762994-222763587	MCF-7	breast:	n/a	n/a
20	BHLHE40	chr1:222762671-222763916	K562	blood:	n/a	n/a
21	POLR2A	chr1:222762853-222763603	ECC-1	luminal epithelium:	n/a	n/a
22	SIN3AK20	chr1:222762876-222763346	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr1:222762858-222763571	PANC-1	pancreas:	n/a	n/a
24	HEY1	chr1:222763050-222763514	HepG2	liver:	n/a	n/a
25	PML	chr1:222763033-222763543	MCF-7	breast:	n/a	n/a
26	SP1	chr1:222762880-222763585	A549	lung:	n/a	n/a
27	CBX3	chr1:222762863-222764109	K562	blood:	n/a	n/a
28	RELA	chr1:222762913-222763772	GM19099	blood:	n/a	n/a
29	POLR2A	chr1:222762977-222763532	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:222762772-222763588	Raji	blood:	n/a	n/a
31	POLR2A	chr1:222762830-222763714	U87	brain:	n/a	n/a
32	ELK1	chr1:222762823-222763423	Hela-S3	cervix:	n/a	n/a
33	MAX	chr1:222762705-222763912	HepG2	liver:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
34	CREB1	chr1:222762941-222763481	A549	lung:	n/a	n/a
35	NFIC	chr1:222763003-222763451	HepG2	liver:	n/a	n/a
36	E2F1	chr1:222763004-222763371	Hela-S3	cervix:	n/a	n/a
37	NR2F2	chr1:222762256-222763834	K562	blood:	n/a	n/a
38	POLR2A	chr1:222762775-222763914	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr1:222762509-222763726	HCT-116	colon:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
40	MAX	chr1:222762892-222763450	H1-hESC	embryonic stem cell:	n/a	chr1:222762906-222762915
41	MAX	chr1:222762679-222763724	ECC-1	luminal epithelium:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
42	STAT5A	chr1:222762881-222763818	K562	blood:	n/a	chr1:222762939-222762950 chr1:222763010-222763022
43	USF1	chr1:222762993-222763256	SK-N-SH_RA	brain:	n/a	n/a
44	GABPA	chr1:222762810-222763765	MCF-7	breast:	n/a	n/a
45	GABPA	chr1:222762810-222763778	SK-N-SH	brain:	n/a	n/a
46	STAT3	chr1:222762993-222763641	GM12878	blood:	n/a	chr1:222763010-222763022
47	MAX	chr1:222762641-222763527	H1-hESC	embryonic stem cell:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
48	SMC3	chr1:222762947-222763516	Hela-S3	cervix:	n/a	n/a
49	REST	chr1:222762964-222763384	SK-N-SH	brain:	n/a	n/a
50	MYC	chr1:222762223-222763947	K562	blood:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842

No.	Distal block	Cell Line	Cell type
1	chr1:222762024..222764722-chr1:222816738..222818394,2	MCF-7	breast:
2	chr1:222762853..222764726-chr1:222816205..222818798,3	MCF-7	breast:
3	chr1:222761959..222766700-chr1:222790061..222794365,7	MCF-7	breast:
4	chr1:222762075..222764721-chr1:222883311..222887470,5	K562	blood:
5	chr1:222760074..222764679-chr1:222790714..222794830,7	K562	blood:
6	chr1:222760324..222764721-chr1:222884429..222887789,6	K562	blood:
7	chr1:222761567..222764879-chr1:222790132..222793494,4	MCF-7	breast:
8	chr1:222761198..222763394-chr1:222816241..222819069,2	K562	blood:
9	chr1:222760723..222765796-chr1:222790714..222795393,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MIA3-2	chr1:222763167-222763304	ENSG00000225265.1

Variant related genes	Relation type
ENSG00000225265	TF binding region
TAF1A	TF binding region
ENSG00000186063	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000162819	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2936028	1.00[AFR][1000 genomes]
rs2936029	1.00[AFR][1000 genomes]
rs2936042	1.00[AFR][1000 genomes]
rs2936043	1.00[AFR][1000 genomes]
rs2936053	1.00[AFR][1000 genomes]
rs3002127	1.00[AFR][1000 genomes]
rs3002135	1.00[AFR][1000 genomes]
rs3002153	1.00[AFR][1000 genomes]
rs3008619	1.00[AFR][1000 genomes]
rs3008636	1.00[AFR][1000 genomes]
rs3008643	1.00[AFR][1000 genomes]
rs3008646	1.00[AFR][1000 genomes]
rs3008648	0.87[AFR][1000 genomes]
rs3008649	1.00[AFR][1000 genomes]
rs35877231	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 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	chr1:222761600-222763800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:222761800-222763800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:222761800-222764200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:222761800-222764200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:222761800-222764200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:222761800-222764200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:222761800-222764600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:222762000-222763600	Active TSS	HMEC	breast
9	chr1:222762000-222763600	Active TSS	K562	blood
10	chr1:222762000-222764000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:222762000-222764200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:222762000-222764200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:222762200-222763400	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr1:222762200-222763600	Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:222762200-222763600	Active TSS	Stomach Mucosa	stomach
16	chr1:222762200-222763600	Active TSS	NHEK	skin
17	chr1:222762200-222763800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:222762200-222763800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:222762200-222763800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:222762200-222763800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:222762200-222763800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:222762200-222763800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:222762200-222763800	Active TSS	A549	lung
24	chr1:222762200-222764000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:222762200-222764000	Active TSS	Ovary	ovary
26	chr1:222762200-222764200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:222762200-222764200	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr1:222762200-222764200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:222762400-222763600	Active TSS	Fetal Stomach	stomach
30	chr1:222762400-222763600	Active TSS	Fetal Thymus	thymus
31	chr1:222762400-222763600	Active TSS	NHDF-Ad	bronchial
32	chr1:222762400-222763800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:222762400-222763800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:222762400-222764000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:222762400-222764000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:222762400-222764000	Active TSS	Fetal Muscle Trunk	muscle
37	chr1:222762400-222764000	Active TSS	Right Atrium	heart
38	chr1:222762400-222764200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:222762600-222763400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:222762600-222763400	Active TSS	NHLF	lung
41	chr1:222762600-222763600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:222762600-222763600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:222762600-222763600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:222762600-222763600	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr1:222762600-222763600	Active TSS	Brain Anterior Caudate	brain
46	chr1:222762600-222763600	Active TSS	Fetal Brain Male	brain
47	chr1:222762600-222763600	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr1:222762600-222763600	Active TSS	Hela-S3	cervix
49	chr1:222762600-222763600	Active TSS	HSMM	muscle
50	chr1:222762600-222763600	Active TSS	HSMMtube	muscle

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