Variant report

Variant	rs28575120
Chromosome Location	chr2:110420500-110420501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:110420332-110421020	HepG2	liver:	n/a	n/a
2	RAD21	chr2:110420311-110420939	MCF-7	breast:	n/a	n/a
3	RAD21	chr2:110420467-110420821	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr2:110420403-110420841	Hela-S3	cervix:	n/a	n/a
5	RAD21	chr2:110420397-110420886	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr2:110420409-110420897	MCF-7	breast:	n/a	n/a
7	SMC3	chr2:110420451-110420863	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr2:110420320-110420938	MCF-7	breast:	n/a	n/a
9	RAD21	chr2:110420447-110420982	HepG2	liver:	n/a	n/a
10	RAD21	chr2:110420473-110420871	A549	lung:	n/a	n/a
11	ZNF143	chr2:110420464-110420818	GM12878	blood:	n/a	n/a
12	CTCF	chr2:110420500-110420650	NHDF-neo	bronchial:	n/a	n/a
13	RAD21	chr2:110420315-110420961	HCT-116	colon:	n/a	n/a
14	CTCF	chr2:110420486-110420890	HCT-116	colon:	n/a	n/a
15	RAD21	chr2:110420470-110420738	GM12878	blood:	n/a	n/a
16	CTCF	chr2:110420500-110420650	GM12869	blood:	n/a	n/a
17	RAD21	chr2:110420435-110420865	GM12878	blood:	n/a	n/a
18	RAD21	chr2:110420389-110420838	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr2:110420371-110420971	HCT-116	colon:	n/a	n/a
20	CTCF	chr2:110420328-110421095	A549	lung:	n/a	n/a
21	CTCF	chr2:110420467-110420983	HepG2	liver:	n/a	n/a
22	RAD21	chr2:110420445-110420849	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr2:110420492-110420672	GM12878	blood:	n/a	n/a
24	RAD21	chr2:110420341-110420927	MCF-7	breast:	n/a	n/a
25	CTCF	chr2:110420492-110420794	MCF-7	breast:	n/a	n/a
26	SMC3	chr2:110420443-110420992	HepG2	liver:	n/a	n/a
27	SMC3	chr2:110420442-110420910	GM12878	blood:	n/a	n/a
28	CTCF	chr2:110420480-110420630	HVMF	connective:	n/a	n/a
29	MYC	chr2:110420402-110422092	MCF10A-Er-Src	breast:	n/a	n/a
30	RAD21	chr2:110420339-110420837	HCT-116	colon:	n/a	n/a
31	RAD21	chr2:110420428-110420764	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr2:110420480-110420705	T-47D	breast:	n/a	n/a
33	CTCF	chr2:110420432-110420862	GM12878	blood:	n/a	n/a
34	RAD21	chr2:110420430-110420798	SK-N-SH_RA	brain:	n/a	n/a
35	CTCF	chr2:110420425-110420803	HepG2	liver:	n/a	n/a
36	CTCF	chr2:110420500-110420650	HAc	cerebellar:	n/a	n/a
37	RAD21	chr2:110420370-110420862	HepG2	liver:	n/a	n/a
38	RAD21	chr2:110420400-110420925	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:110303360..110304330-chr2:110420115..110421127,10	MCF-7	breast:
2	chr2:110303351..110304315-chr2:110420246..110421095,4	MCF-7	breast:
3	chr2:110373051..110373767-chr2:110420369..110421113,2	MCF-7	breast:
4	chr2:110370616..110372682-chr2:110420303..110422554,4	MCF-7	breast:
5	chr2:110368590..110369642-chr2:110420274..110420998,3	MCF-7	breast:

No data

Variant related genes	Relation type
BMS1P19	TF binding region
ENSG00000230603	TF binding region
ENSG00000198142	Chromatin interaction
ENSG00000186522	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1010840	0.95[ASN][1000 genomes]
rs1036316	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11691252	0.95[ASN][1000 genomes]
rs11694695	0.95[ASN][1000 genomes]
rs13029553	0.95[ASN][1000 genomes]
rs34205087	0.95[ASN][1000 genomes]
rs62151706	0.81[AMR][1000 genomes]
rs62151707	0.82[AMR][1000 genomes]
rs72826839	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7591413	0.95[ASN][1000 genomes]
rs919943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
8	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv999552	chr2:110396395-110978224	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110417600-110421800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:110417800-110421800	Enhancers	HepG2	liver
3	chr2:110418000-110420600	Weak transcription	Hela-S3	cervix
4	chr2:110418200-110420800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:110418400-110420800	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:110418400-110421800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:110420400-110420600	Enhancers	Placenta	Placenta
8	chr2:110420400-110421000	Enhancers	Esophagus	oesophagus
9	chr2:110420400-110421600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:110420400-110421800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:110420400-110422000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:110420400-110422000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:110420400-110422000	Enhancers	Fetal Brain Male	brain
14	chr2:110420400-110422000	Enhancers	NHEK	skin
15	chr2:110420400-110425000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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