Variant report

Variant	rs28812293
Chromosome Location	chr2:110369568-110369569
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	FOS	chr2:110369272-110369827	MCF10A-Er-Src	breast:	n/a	n/a
2	RCOR1	chr2:110369142-110369718	Hela-S3	cervix:	n/a	n/a
3	RAD21	chr2:110369146-110369654	MCF-7	breast:	n/a	n/a
4	MYC	chr2:110369342-110370022	MCF10A-Er-Src	breast:	n/a	n/a
5	RAD21	chr2:110369185-110370139	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr2:110369085-110379088	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:110369375-110369794	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr2:110369266-110369792	MCF10A-Er-Src	breast:	n/a	n/a
9	SMC3	chr2:110369210-110369615	HepG2	liver:	n/a	n/a
10	ZKSCAN1	chr2:110369249-110369632	Hela-S3	cervix:	n/a	n/a
11	MAX	chr2:110369141-110369673	Hela-S3	cervix:	n/a	n/a
12	ARID3A	chr2:110369207-110370805	HepG2	liver:	n/a	n/a
13	SMC3	chr2:110369132-110369637	Hela-S3	cervix:	n/a	n/a
14	BRCA1	chr2:110369558-110370993	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr2:110369209-110369597	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:110369276-110373158	IMR90	lung:	n/a	n/a
17	E2F4	chr2:110369413-110372380	MCF10A-Er-Src	breast:	n/a	chr2:110371142-110371152 chr2:110370860-110370874 chr2:110370863-110370870 chr2:110370862-110370871 chr2:110370863-110370870 chr2:110370863-110370870 chr2:110370859-110370871 chr2:110371199-110371211 chr2:110370968-110370978 chr2:110371209-110371219 chr2:110371309-110371321
18	CEBPB	chr2:110369275-110369873	IMR90	lung:	n/a	n/a
19	MYC	chr2:110369348-110370054	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr2:110369422-110372500	Hela-S3	cervix:	n/a	n/a
21	MAFK	chr2:110369427-110369832	IMR90	lung:	n/a	n/a
22	KAP1	chr2:110369175-110369898	HEK293	kidney:	n/a	n/a
23	CTCF	chr2:110369440-110369590	A549	lung:	n/a	n/a
24	POLR2A	chr2:110369410-110372842	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr2:110369155-110369716	HCT-116	colon:	n/a	n/a
26	CTCF	chr2:110369160-110369570	HepG2	liver:	n/a	n/a
27	CEBPB	chr2:110369274-110369736	Hela-S3	cervix:	n/a	n/a
28	STAT3	chr2:110369257-110369828	MCF10A-Er-Src	breast:	n/a	n/a
29	CHD1	chr2:110369172-110374773	IMR90	lung:	n/a	n/a
30	RAD21	chr2:110369165-110369581	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr2:110369129-110369586	MCF-7	breast:	n/a	n/a
32	FOS	chr2:110369362-110369744	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr2:110369290-110378742	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr2:110369265-110369906	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr2:110369269-110370016	MCF10A-Er-Src	breast:	n/a	n/a
36	EP300	chr2:110369333-110369796	GM12878	blood:	n/a	n/a
37	RAD21	chr2:110369036-110369749	HCT-116	colon:	n/a	n/a
38	RAD21	chr2:110369136-110369730	MCF-7	breast:	n/a	n/a
39	POLR2A	chr2:110369133-110370469	PANC-1	pancreas:	n/a	n/a
40	RAD21	chr2:110369125-110369700	HepG2	liver:	n/a	n/a
41	CTCF	chr2:110369420-110369570	GM12865	blood:	n/a	n/a
42	RAD21	chr2:110369182-110369604	GM12878	blood:	n/a	n/a
43	RAD21	chr2:110369151-110369604	A549	lung:	n/a	n/a
44	STAT3	chr2:110369340-110370231	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:110369302..110370206-chr2:110472595..110473565,2	MCF-7	breast:
2	chr2:110362640..110365155-chr2:110368934..110372656,4	MCF-7	breast:
3	chr2:110368590..110369642-chr2:110420274..110420998,3	MCF-7	breast:
4	chr2:110368286..110370966-chr2:110371073..110372751,2	MCF-7	breast:
5	chr1:150131401..150134100-chr2:110369407..110372211,2	MCF-7	breast:

Variant related genes	Relation type
SOWAHC	TF binding region
ENSG00000198142	Chromatin interaction
ENSG00000230696	Chromatin interaction
ENSG00000186522	Chromatin interaction
ENSG00000023902	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12719999	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1434168	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28477948	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28513171	0.82[ASN][1000 genomes]
rs28520382	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28526306	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28634501	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2903537	0.87[ASN][1000 genomes]
rs4953844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594051	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6594052	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6732116	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72627488	0.84[ASN][1000 genomes]
rs9330313	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9330315	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9330326	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9330327	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9678113	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9751647	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9751995	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9752241	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs990967	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv829617	chr2:110359857-110380012	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
2	chr2:110358800-110370200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:110359800-110370200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:110359800-110370600	Weak transcription	Brain Angular Gyrus	brain
5	chr2:110362400-110370200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:110362600-110370400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:110363800-110369800	Weak transcription	Right Ventricle	heart
8	chr2:110366000-110370400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:110367200-110370000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:110367600-110369600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:110367600-110369600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:110367600-110369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:110367800-110369800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:110367800-110369800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:110368000-110370200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:110368000-110370800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:110368400-110370200	Enhancers	Liver	Liver
18	chr2:110368400-110370200	Enhancers	Colon Smooth Muscle	Colon
19	chr2:110368600-110369600	Flanking Active TSS	Hela-S3	cervix
20	chr2:110368600-110369800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:110368600-110371200	Active TSS	GM12878-XiMat	blood
22	chr2:110368800-110369800	Enhancers	Fetal Heart	heart
23	chr2:110369000-110369600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:110369000-110369600	Enhancers	Ovary	ovary
25	chr2:110369000-110370000	Flanking Active TSS	NHEK	skin
26	chr2:110369000-110370200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:110369000-110370200	Enhancers	Psoas Muscle	Psoas
28	chr2:110369000-110373000	Active TSS	NHLF	lung
29	chr2:110369000-110373800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:110369200-110369600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:110369200-110369600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:110369200-110369600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:110369200-110369600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:110369200-110369600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:110369200-110369600	Enhancers	Adipose Nuclei	Adipose
36	chr2:110369200-110369600	Enhancers	Left Ventricle	heart
37	chr2:110369200-110369600	Enhancers	Right Atrium	heart
38	chr2:110369200-110369800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr2:110369200-110369800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr2:110369200-110369800	Enhancers	Brain Hippocampus Middle	brain
41	chr2:110369200-110369800	Enhancers	Fetal Brain Female	brain
42	chr2:110369200-110369800	Enhancers	Fetal Stomach	stomach
43	chr2:110369200-110369800	Enhancers	Placenta Amnion	Placenta Amnion
44	chr2:110369200-110369800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr2:110369200-110370000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:110369200-110370000	Enhancers	Fetal Lung	lung
47	chr2:110369200-110370000	Flanking Active TSS	HMEC	breast
48	chr2:110369200-110370000	Flanking Active TSS	NH-A	brain
49	chr2:110369200-110370200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:110369200-110370200	Enhancers	Duodenum Mucosa	Duodenum

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