Variant report

Variant	rs73058371
Chromosome Location	chr1:185703413-185703414
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	TCF7L2	chr1:185702829-185703813	HCT-116	colon:	n/a	chr1:185703047-185703063 chr1:185703050-185703059 chr1:185703048-185703062 chr1:185703047-185703063 chr1:185703047-185703061
2	ZKSCAN1	chr1:185703074-185703908	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:185703212-185703817	U87	brain:	n/a	n/a
4	NFYA	chr1:185703278-185703591	Hela-S3	cervix:	n/a	chr1:185703442-185703460 chr1:185703442-185703456 chr1:185703442-185703457 chr1:185703442-185703455 chr1:185703442-185703457 chr1:185703441-185703453 chr1:185703444-185703454
5	ZNF263	chr1:185701992-185703999	HEK293-T-REx	kidney:	n/a	chr1:185702875-185702884
6	MAX	chr1:185703206-185703729	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:185703183-185703632	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:185703374-185703774	IMR90	lung:	n/a	n/a
9	TFAP2A	chr1:185702925-185704040	Hela-S3	cervix:	n/a	chr1:185703603-185703611 chr1:185703600-185703612 chr1:185703600-185703612 chr1:185703600-185703612 chr1:185703600-185703612 chr1:185703603-185703611 chr1:185703581-185703593 chr1:185703599-185703614 chr1:185703603-185703611 chr1:185703583-185703593
10	RFX5	chr1:185702945-185703608	Hela-S3	cervix:	n/a	chr1:185703445-185703454
11	POLR2A	chr1:185703004-185703802	MCF-7	breast:	n/a	n/a
12	FOXA2	chr1:185702956-185703633	A549	lung:	n/a	n/a
13	TEAD4	chr1:185702904-185703547	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOXA1	chr1:185703016-185703540	HepG2	liver:	n/a	chr1:185703284-185703299
15	TBP	chr1:185702941-185703706	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:185703371-185703708	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr1:185702640-185704258	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr1:185702976-185703959	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAFK	chr1:185703218-185703884	Hela-S3	cervix:	n/a	n/a
20	MAX	chr1:185702645-185703645	Hela-S3	cervix:	n/a	n/a
21	TBP	chr1:185703178-185703605	Hela-S3	cervix:	n/a	n/a
22	MAX	chr1:185702910-185703713	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF7	chr1:185703217-185703721	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr1:185703380-185703530	K562	blood:	n/a	n/a
25	GATA2	chr1:185702655-185704049	SH-SY5Y	brain:	n/a	n/a
26	TAF1	chr1:185703193-185703843	H1-hESC	embryonic stem cell:	n/a	n/a
27	GATA3	chr1:185702724-185703731	SK-N-SH	brain:	n/a	n/a
28	CREB1	chr1:185703317-185703587	A549	lung:	n/a	n/a
29	MAX	chr1:185702929-185703739	H1-hESC	embryonic stem cell:	n/a	n/a
30	JUND	chr1:185702752-185703856	H1-hESC	embryonic stem cell:	n/a	chr1:185703446-185703455
31	RCOR1	chr1:185702948-185703424	K562	blood:	n/a	n/a
32	TAF1	chr1:185703298-185703669	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr1:185703380-185703530	HA-sp	spinal cord:	n/a	n/a
34	POLR2A	chr1:185703079-185703725	HUVEC	blood vessel:	n/a	n/a
35	TCF7L2	chr1:185702854-185703497	HEK293	kidney:	n/a	chr1:185703047-185703063 chr1:185703050-185703059 chr1:185703048-185703062 chr1:185703047-185703063 chr1:185703047-185703061
36	BRCA1	chr1:185703047-185703481	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:185703177-185703679	U87	brain:	n/a	n/a
38	NFYB	chr1:185703284-185703642	K562	blood:	n/a	chr1:185703442-185703456 chr1:185703442-185703457 chr1:185703442-185703455 chr1:185703442-185703457 chr1:185703441-185703453 chr1:185703444-185703454 chr1:185703439-185703454
39	BACH1	chr1:185703127-185703543	H1-hESC	embryonic stem cell:	n/a	n/a
40	GATA3	chr1:185702585-185703736	MCF-7	breast:	n/a	n/a
41	GATA3	chr1:185702719-185703487	MCF-7	breast:	n/a	n/a
42	MAZ	chr1:185702992-185703573	Hela-S3	cervix:	n/a	n/a
43	TCF7L2	chr1:185702840-185703718	PANC-1	pancreas:	n/a	chr1:185703047-185703063 chr1:185703050-185703059 chr1:185703048-185703062 chr1:185703047-185703063 chr1:185703047-185703061
44	FOXA1	chr1:185703007-185703505	HepG2	liver:	n/a	chr1:185703284-185703299
45	CTCF	chr1:185703304-185703522	A549	lung:	n/a	n/a
46	E2F6	chr1:185702929-185703658	H1-hESC	embryonic stem cell:	n/a	chr1:185703547-185703557 chr1:185703444-185703453 chr1:185703598-185703608
47	CTCF	chr1:185702753-185703563	A549	lung:	n/a	chr1:185703097-185703115 chr1:185703092-185703113
48	CTCF	chr1:185703409-185703495	MCF-7	breast:	n/a	n/a
49	POLR2A	chr1:185703334-185703641	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr1:185703211-185703686	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
HMCN1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs28507443	0.82[AFR][1000 genomes]
rs28571005	0.82[AFR][1000 genomes]
rs57646071	0.82[AFR][1000 genomes]
rs61492840	0.82[AFR][1000 genomes]
rs6701269	0.85[AFR][1000 genomes]
rs6703750	0.82[AFR][1000 genomes]
rs73058365	0.87[AFR][1000 genomes]
rs73058381	0.82[AFR][1000 genomes]
rs73060472	0.82[AFR][1000 genomes]
rs73060496	0.82[AFR][1000 genomes]
rs73062507	0.82[AFR][1000 genomes]
rs73070566	0.82[AFR][1000 genomes]
rs73070580	0.82[AFR][1000 genomes]
rs73070592	0.82[AFR][1000 genomes]
rs73070595	0.82[AFR][1000 genomes]
rs73072044	0.82[AFR][1000 genomes]
rs73072053	0.82[AFR][1000 genomes]
rs73072054	0.82[AFR][1000 genomes]
rs9727715	0.82[AFR][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	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185702400-185704200	Active TSS	Fetal Kidney	kidney
2	chr1:185702600-185703800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr1:185702600-185704000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:185702600-185704400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:185702600-185704600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:185702600-185705400	Active TSS	Aorta	Aorta
7	chr1:185702800-185703600	Active TSS	Muscle Satellite Cultured Cells	--
8	chr1:185702800-185703600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:185702800-185703600	Active TSS	Duodenum Mucosa	Duodenum
10	chr1:185702800-185703800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:185702800-185703800	Active TSS	Brain Cingulate Gyrus	brain
12	chr1:185702800-185703800	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr1:185702800-185703800	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr1:185702800-185703800	Active TSS	Hela-S3	cervix
15	chr1:185702800-185703800	Active TSS	Osteobl	bone
16	chr1:185702800-185704000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:185702800-185704000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:185702800-185704000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:185702800-185704000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:185702800-185704000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:185702800-185704000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr1:185702800-185704000	Active TSS	Brain Substantia Nigra	brain
23	chr1:185702800-185704000	Active TSS	Fetal Brain Female	brain
24	chr1:185702800-185704000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:185702800-185704000	Bivalent/Poised TSS	A549	lung
26	chr1:185702800-185704400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:185702800-185704400	Active TSS	Fetal Lung	lung
28	chr1:185702800-185704400	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:185702800-185704600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:185702800-185704800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:185702800-185704800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:185702800-185704800	Active TSS	Brain Hippocampus Middle	brain
33	chr1:185702800-185705000	Active TSS	H9 Cell Line	embryonic stem cell
34	chr1:185702800-185705000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:185702800-185705200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr1:185702800-185705200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:185702800-185705200	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:185702800-185705200	Flanking Active TSS	HMEC	breast
39	chr1:185702800-185705400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:185702800-185705400	Flanking Active TSS	HUVEC	blood vessel
41	chr1:185702800-185706400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:185703000-185703600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:185703000-185703600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
44	chr1:185703000-185703800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:185703000-185703800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:185703000-185703800	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr1:185703000-185703800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
48	chr1:185703000-185703800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
49	chr1:185703000-185703800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr1:185703000-185703800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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