Variant report

Variant	rs2577154
Chromosome Location	chr1:220267599-220267600
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	NFIC	chr1:220267400-220267791	HepG2	liver:	n/a	n/a
2	HEY1	chr1:220267391-220267955	HepG2	liver:	n/a	chr1:220267517-220267532
3	TCF7L2	chr1:220267564-220268117	Hela-S3	cervix:	n/a	n/a
4	SIN3AK20	chr1:220267380-220268104	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:220267325-220268171	MCF10A-Er-Src	breast:	n/a	n/a
6	YY1	chr1:220267205-220267670	SK-N-SH_RA	brain:	n/a	chr1:220267312-220267321 chr1:220267409-220267418 chr1:220267520-220267531
7	BHLHE40	chr1:220266921-220268193	K562	blood:	n/a	chr1:220267334-220267350 chr1:220267337-220267353 chr1:220267870-220267886
8	TAF1	chr1:220267287-220267964	HepG2	liver:	n/a	n/a
9	GABPA	chr1:220267273-220267622	HepG2	liver:	n/a	chr1:220267409-220267418 chr1:220267312-220267321
10	MAX	chr1:220266819-220268414	HCT-116	colon:	n/a	chr1:220267928-220267938 chr1:220267410-220267420
11	TAF7	chr1:220267347-220267960	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr1:220267271-220268060	H1-hESC	embryonic stem cell:	n/a	chr1:220267928-220267938 chr1:220267410-220267420
13	SP1	chr1:220267245-220267755	GM12878	blood:	n/a	chr1:220267408-220267418 chr1:220267409-220267418 chr1:220267311-220267320 chr1:220267330-220267342 chr1:220267312-220267321 chr1:220267435-220267444 chr1:220267310-220267322 chr1:220267332-220267341 chr1:220267435-220267444 chr1:220267434-220267446 chr1:220267434-220267445 chr1:220267408-220267417 chr1:220267436-220267445 chr1:220267407-220267419 chr1:220267331-220267340 chr1:220267408-220267417 chr1:220267330-220267342 chr1:220267435-220267449 chr1:220267498-220267509 chr1:220267407-220267419 chr1:220267408-220267418 chr1:220267408-220267422 chr1:220267311-220267320
14	JUND	chr1:220267178-220267690	A549	lung:	n/a	chr1:220267333-220267342
15	CHD1	chr1:220267510-220268040	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:220267277-220268015	GM18526	blood:	n/a	n/a
17	POLR2A	chr1:220267382-220267934	HCT-116	colon:	n/a	n/a
18	ZNF143	chr1:220267040-220267934	H1-hESC	embryonic stem cell:	n/a	chr1:220267303-220267321 chr1:220267443-220267461
19	POLR2A	chr1:220267300-220268250	HCT-116	colon:	n/a	n/a
20	ZNF143	chr1:220267202-220268132	GM12878	blood:	n/a	chr1:220267303-220267321 chr1:220267443-220267461
21	EBF1	chr1:220267264-220268079	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:220267371-220267884	GM12892	blood:	n/a	n/a
23	SP1	chr1:220266792-220268273	HCT-116	colon:	n/a	chr1:220267408-220267418 chr1:220267409-220267418 chr1:220267311-220267320 chr1:220267330-220267342 chr1:220267312-220267321 chr1:220267435-220267444 chr1:220267310-220267322 chr1:220267332-220267341 chr1:220267435-220267444 chr1:220267924-220267938 chr1:220267434-220267446 chr1:220267434-220267445 chr1:220267929-220267938 chr1:220267408-220267417 chr1:220267928-220267937 chr1:220267436-220267445 chr1:220267407-220267419 chr1:220267331-220267340 chr1:220267408-220267417 chr1:220267330-220267342 chr1:220267927-220267939 chr1:220267435-220267449 chr1:220267831-220267843 chr1:220267498-220267509 chr1:220267407-220267419 chr1:220267408-220267418 chr1:220267928-220267938 chr1:220267927-220267939 chr1:220267832-220267841 chr1:220267408-220267422 chr1:220267311-220267320
24	ZEB1	chr1:220267171-220267948	GM12878	blood:	n/a	n/a
25	ETS1	chr1:220267272-220268034	K562	blood:	n/a	chr1:220267409-220267420 chr1:220267333-220267344
26	MYC	chr1:220267348-220268148	H1-hESC	embryonic stem cell:	n/a	chr1:220267928-220267938 chr1:220267410-220267420
27	POLR2A	chr1:220267265-220268056	MCF-7	breast:	n/a	n/a
28	EP300	chr1:220267379-220267806	GM12878	blood:	n/a	n/a
29	YY1	chr1:220267204-220268049	K562	blood:	n/a	chr1:220267312-220267321 chr1:220267409-220267418 chr1:220267520-220267531
30	POLR2A	chr1:220267331-220268019	PFSK-1	brain:	n/a	n/a
31	MAX	chr1:220267429-220268177	H1-hESC	embryonic stem cell:	n/a	chr1:220267928-220267938
32	GABPA	chr1:220267276-220267873	SK-N-SH	brain:	n/a	chr1:220267409-220267418 chr1:220267312-220267321
33	SP1	chr1:220266852-220268193	HCT-116	colon:	n/a	chr1:220267408-220267418 chr1:220267409-220267418 chr1:220267311-220267320 chr1:220267330-220267342 chr1:220267312-220267321 chr1:220267435-220267444 chr1:220267310-220267322 chr1:220267332-220267341 chr1:220267435-220267444 chr1:220267924-220267938 chr1:220267434-220267446 chr1:220267434-220267445 chr1:220267929-220267938 chr1:220267408-220267417 chr1:220267928-220267937 chr1:220267436-220267445 chr1:220267407-220267419 chr1:220267331-220267340 chr1:220267408-220267417 chr1:220267330-220267342 chr1:220267927-220267939 chr1:220267435-220267449 chr1:220267831-220267843 chr1:220267498-220267509 chr1:220267407-220267419 chr1:220267408-220267418 chr1:220267928-220267938 chr1:220267927-220267939 chr1:220267832-220267841 chr1:220267408-220267422 chr1:220267311-220267320
34	NRF1	chr1:220267212-220267619	GM12878	blood:	n/a	chr1:220267409-220267418 chr1:220267312-220267321
35	POLR2A	chr1:220267335-220268142	Hela-S3	cervix:	n/a	n/a
36	SIN3AK20	chr1:220267281-220268045	H1-hESC	embryonic stem cell:	n/a	n/a
37	SIN3AK20	chr1:220267370-220267700	PANC-1	pancreas:	n/a	n/a
38	MAX	chr1:220267058-220268098	GM12878	blood:	n/a	chr1:220267928-220267938 chr1:220267410-220267420
39	GABPA	chr1:220267089-220267918	MCF-7	breast:	n/a	chr1:220267409-220267418 chr1:220267312-220267321
40	CEBPB	chr1:220267451-220268119	Hela-S3	cervix:	n/a	n/a
41	TCF12	chr1:220267259-220268071	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr1:220267262-220267863	U87	brain:	n/a	n/a
43	NR2F2	chr1:220266546-220268210	K562	blood:	n/a	n/a
44	SIN3AK20	chr1:220267246-220268311	MCF-7	breast:	n/a	n/a
45	YY1	chr1:220267088-220267994	HepG2	liver:	n/a	chr1:220267312-220267321 chr1:220267409-220267418 chr1:220267520-220267531
46	MAX	chr1:220267260-220268294	A549	lung:	n/a	chr1:220267928-220267938 chr1:220267410-220267420
47	SP4	chr1:220267183-220267782	H1-hESC	embryonic stem cell:	n/a	chr1:220267407-220267423 chr1:220267434-220267445 chr1:220267405-220267421 chr1:220267434-220267450 chr1:220267498-220267509 chr1:220267330-220267346
48	TBL1XR1	chr1:220267300-220267805	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:220267380-220268100	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr1:220267354-220267945	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220267529..220269249-chr1:220275235..220276981,2	K562	blood:
2	chr1:220260533..220264899-chr1:220265232..220269626,12	MCF-7	breast:
3	chr1:220218535..220220494-chr1:220265581..220269628,4	MCF-7	breast:
4	chr1:220090768..220093296-chr1:220265981..220268772,2	K562	blood:
5	chr1:220261171..220264758-chr1:220266195..220270505,9	MCF-7	breast:
6	chr1:220266934..220269601-chr1:220286713..220289289,2	K562	blood:
7	chr1:220266934..220268710-chr1:220286713..220288993,3	K562	blood:
8	chr1:220215698..220221065-chr1:220265352..220268996,5	K562	blood:
9	chr1:220219736..220221759-chr1:220265959..220267842,3	K562	blood:
10	chr1:220266254..220269129-chr1:220290209..220292443,2	MCF-7	breast:
11	chr1:220218169..220221765-chr1:220261064..220269153,11	MCF-7	breast:
12	chr1:220267309..220268289-chrX:55744121..55744662,2	Hela-S3	cervix:

Variant related genes	Relation type
BPNT1	TF binding region
ENSG00000162813	Chromatin interaction
ENSG00000207590	Chromatin interaction
ENSG00000196660	Chromatin interaction
ENSG00000136628	Chromatin interaction
ENSG00000083750	Chromatin interaction
ENSG00000207624	Chromatin interaction
ENSG00000067704	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1611863	0.89[AMR][1000 genomes]
rs2577135	0.89[AMR][1000 genomes]
rs2577153	0.88[AFR][1000 genomes]
rs2647472	1.00[AMR][1000 genomes]
rs2789785	0.89[AMR][1000 genomes]
rs7524161	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 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	chr1:220264000-220267800	Weak transcription	Fetal Heart	heart
2	chr1:220266400-220267800	Active TSS	HepG2	liver
3	chr1:220266800-220267600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:220266800-220268000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:220266800-220268400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:220266800-220268400	Active TSS	Brain Germinal Matrix	brain
7	chr1:220266800-220268400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:220266800-220268400	Active TSS	Right Atrium	heart
9	chr1:220266800-220268600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:220266800-220268600	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:220266800-220268800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:220266800-220269000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:220267000-220268000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:220267000-220268000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:220267000-220268000	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr1:220267000-220268000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:220267000-220268000	Active TSS	Brain Angular Gyrus	brain
18	chr1:220267000-220268000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:220267000-220268000	Active TSS	Fetal Brain Male	brain
20	chr1:220267000-220268000	Active TSS	Fetal Brain Female	brain
21	chr1:220267000-220268000	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr1:220267000-220268000	Active TSS	Stomach Smooth Muscle	stomach
23	chr1:220267000-220268200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:220267000-220268200	Active TSS	Colon Smooth Muscle	Colon
25	chr1:220267000-220268200	Active TSS	Fetal Lung	lung
26	chr1:220267000-220268200	Active TSS	Fetal Stomach	stomach
27	chr1:220267000-220268200	Active TSS	Psoas Muscle	Psoas
28	chr1:220267000-220268200	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr1:220267000-220268200	Active TSS	Hela-S3	cervix
30	chr1:220267000-220268200	Active TSS	HSMMtube	muscle
31	chr1:220267000-220268200	Active TSS	Osteobl	bone
32	chr1:220267000-220268400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:220267000-220268400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:220267000-220268400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:220267000-220268400	Active TSS	Brain Hippocampus Middle	brain
36	chr1:220267000-220268400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:220267000-220268400	Active TSS	Fetal Kidney	kidney
38	chr1:220267000-220268400	Active TSS	Left Ventricle	heart
39	chr1:220267000-220268400	Active TSS	Ovary	ovary
40	chr1:220267000-220268400	Active TSS	Right Ventricle	heart
41	chr1:220267000-220268600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:220267000-220268600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr1:220267000-220268800	Active TSS	NHDF-Ad	bronchial
44	chr1:220267000-220269000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:220267000-220269000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:220267000-220269000	Active TSS	HMEC	breast
47	chr1:220267000-220269200	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr1:220267200-220267600	Active TSS	Primary hematopoietic stem cells	blood
49	chr1:220267200-220267600	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr1:220267200-220267800	Active TSS	Primary neutrophils fromperipheralblood	blood

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