Variant report

Variant	rs1902100
Chromosome Location	chr5:42912313-42912314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:42912289-42912677	A549	lung:	n/a	n/a
2	RAD21	chr5:42912163-42912935	HCT-116	colon:	n/a	n/a
3	RAD21	chr5:42912285-42912588	HepG2	liver:	n/a	n/a
4	RAD21	chr5:42912221-42912700	HepG2	liver:	n/a	n/a
5	MAFK	chr5:42912275-42912737	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr5:42912280-42912430	A549	lung:	n/a	n/a
7	CTCF	chr5:42912190-42912789	HCT-116	colon:	n/a	n/a
8	CTCF	chr5:42912311-42912559	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr5:42912294-42912774	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr5:42912152-42912907	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr5:42912270-42912470	MCF10A-Er-Src	breast:	n/a	n/a
12	RFX5	chr5:42912167-42912666	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr5:42912297-42912682	GM12878	blood:	n/a	n/a
14	CTCF	chr5:42912260-42912410	HAc	cerebellar:	n/a	n/a
15	RAD21	chr5:42912185-42912847	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr5:42912310-42912742	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr5:42912228-42912906	HCT-116	colon:	n/a	n/a
18	RAD21	chr5:42912305-42912667	A549	lung:	n/a	n/a
19	CTCF	chr5:42912083-42912902	A549	lung:	n/a	n/a
20	CTCF	chr5:42912294-42912750	K562	blood:	n/a	n/a
21	RAD21	chr5:42912132-42912885	MCF-7	breast:	n/a	n/a
22	CTCF	chr5:42912258-42912755	MCF-7	breast:	n/a	n/a
23	RAD21	chr5:42912263-42912923	A549	lung:	n/a	n/a
24	RAD21	chr5:42912227-42912819	MCF-7	breast:	n/a	n/a
25	CTCF	chr5:42912281-42912755	IMR90	lung:	n/a	n/a
26	PRDM1	chr5:42912281-42912646	Hela-S3	cervix:	n/a	chr5:42912458-42912473
27	CTCF	chr5:42912254-42912684	A549	lung:	n/a	n/a
28	CTCF	chr5:42912292-42912683	T-47D	breast:	n/a	n/a
29	CTCF	chr5:42912115-42912976	HCT-116	colon:	n/a	n/a
30	RAD21	chr5:42912207-42912846	IMR90	lung:	n/a	n/a
31	SMC3	chr5:42912060-42912895	Hela-S3	cervix:	n/a	n/a
32	RAD21	chr5:42912253-42912925	A549	lung:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:42911324..42913004-chr5:43008845..43010689,2	K562	blood:
2	chr5:42912144..42912799-chr5:43065004..43065795,2	K562	blood:
3	chr5:42910969..42913482-chr5:43041756..43043482,2	K562	blood:
4	chr5:42910607..42912448-chr5:43007420..43009713,2	MCF-7	breast:
5	chr5:42911041..42912693-chr5:42987765..42989682,2	K562	blood:
6	chr5:42912044..42912956-chr5:43015192..43016130,2	MCF-7	breast:
7	chr5:42910198..42912584-chr5:43010319..43012445,2	MCF-7	breast:
8	chr5:42911247..42912986-chr5:43038290..43040466,2	MCF-7	breast:
9	chr5:42912159..42915403-chr5:43007665..43011079,4	MCF-7	breast:
10	chr5:42912188..42912778-chr5:43389546..43390532,2	MCF-7	breast:
11	chr5:42910969..42913867-chr5:43041026..43043256,2	K562	blood:
12	chr5:42907363..42912501-chr5:43064737..43069149,8	MCF-7	breast:
13	chr5:42910815..42912659-chr5:43063586..43066897,3	K562	blood:
14	chr5:42901499..42902521-chr5:42911994..42912667,4	MCF-7	breast:
15	chr5:42911987..42912980-chr5:42970878..42972001,4	MCF-7	breast:
16	chr5:42912040..42912962-chr5:43105448..43106382,6	MCF-7	breast:
17	chr5:42911638..42913879-chr5:42921699..42924243,2	K562	blood:
18	chr5:42909564..42912541-chr5:42988182..42990519,2	K562	blood:
19	chr5:42912223..42913017-chr5:43105562..43106421,4	MCF-7	breast:
20	chr5:42911199..42912875-chr5:42913182..42914801,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000251656	TF binding region
ENSG00000177738	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10036147	0.98[ASN][1000 genomes]
rs10036468	0.98[ASN][1000 genomes]
rs10044301	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053947	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061198	0.98[ASN][1000 genomes]
rs10068961	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072017	0.92[ASN][1000 genomes]
rs12655096	1.00[ASN][1000 genomes]
rs12658770	0.95[ASN][1000 genomes]
rs12659760	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156119	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354920	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160330	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs188793	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2098715	0.91[ASN][1000 genomes]
rs2548362	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548364	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2548365	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2548366	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2603622	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603624	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28415991	1.00[ASN][1000 genomes]
rs309932	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309934	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309935	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309942	0.87[EUR][1000 genomes]
rs315246	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315253	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315263	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34917335	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34981544	0.98[ASN][1000 genomes]
rs371261	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs378235	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs378344	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs388214	0.89[ASN][1000 genomes]
rs420550	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs435312	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs446294	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4482913	0.98[ASN][1000 genomes]
rs4513706	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453436	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451649	0.98[ASN][1000 genomes]
rs6451650	0.98[ASN][1000 genomes]
rs6451651	0.98[ASN][1000 genomes]
rs6451652	0.98[ASN][1000 genomes]
rs6451653	0.94[ASN][1000 genomes]
rs6451654	0.94[ASN][1000 genomes]
rs6864892	0.91[ASN][1000 genomes]
rs6867854	0.94[ASN][1000 genomes]
rs6875237	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6881608	0.98[ASN][1000 genomes]
rs6885355	0.98[ASN][1000 genomes]
rs6886626	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6895458	0.98[ASN][1000 genomes]
rs6895751	0.98[ASN][1000 genomes]
rs71627562	0.92[ASN][1000 genomes]
rs71627563	0.92[ASN][1000 genomes]
rs7701142	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7721545	0.89[ASN][1000 genomes]
rs9885101	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
7	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
8	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv980936	chr5:42894375-42930741	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv968909	chr5:42903982-42953465	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1806082	chr5:42906572-42967215	Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42909400-42912400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:42909400-42915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:42909600-42912400	Weak transcription	A549	lung
4	chr5:42909600-42913000	Weak transcription	Primary T cells fromperipheralblood	blood

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