Variant report

Variant	rs72933939
Chromosome Location	chr18:29027419-29027420
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	chr18:29027295-29027887	MCF10A-Er-Src	breast:	n/a	chr18:29027347-29027359
2	POLR2A	chr18:29027272-29034683	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr18:29027053-29027906	MCF10A-Er-Src	breast:	n/a	chr18:29027647-29027656
4	FOS	chr18:29027316-29027812	MCF10A-Er-Src	breast:	n/a	chr18:29027347-29027359
5	STAT3	chr18:29027344-29027838	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr18:29026954-29028137	K562	blood:	n/a	chr18:29027959-29027968 chr18:29027959-29027968 chr18:29027957-29027970 chr18:29027959-29027970 chr18:29027139-29027150 chr18:29027959-29027968 chr18:29027959-29027968 chr18:29027957-29027968 chr18:29027139-29027150 chr18:29027957-29027970
7	FOS	chr18:29027412-29027836	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr18:29027265-29032185	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr18:29027387-29027844	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr18:29027345-29027833	MCF10A-Er-Src	breast:	n/a	chr18:29027647-29027656

Variant related genes	Relation type
DSG3	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16961994	1.00[AMR][1000 genomes]
rs66889852	1.00[EUR][1000 genomes]
rs67423158	0.89[EUR][1000 genomes]
rs68094756	1.00[EUR][1000 genomes]
rs7240573	0.89[EUR][1000 genomes]
rs7240789	0.89[EUR][1000 genomes]
rs7241611	0.89[EUR][1000 genomes]
rs72922886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72922892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925127	0.89[EUR][1000 genomes]
rs72925129	0.89[EUR][1000 genomes]
rs72925137	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72925140	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72925152	1.00[AMR][1000 genomes]
rs72925153	1.00[AMR][1000 genomes]
rs72925155	1.00[AMR][1000 genomes]
rs72925156	1.00[AMR][1000 genomes]
rs72925163	1.00[AMR][1000 genomes]
rs72929966	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929968	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72931998	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932001	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72933906	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1060592	chr18:28965770-29042332	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1059676	chr18:28965770-29049614	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv869902	chr18:28967184-29053244	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv524890	chr18:28967410-29056465	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv576630	chr18:28969044-29049018	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv576631	chr18:28969044-29051677	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv458045	chr18:28969044-29056465	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv576632	chr18:28969044-29056465	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv2751776	chr18:28970147-29057719	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv576633	chr18:28972363-29038123	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv576634	chr18:28972363-29049018	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1065809	chr18:28974612-29035411	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1065570	chr18:28974612-29049614	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1058214	chr18:28974612-29053891	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1062970	chr18:28976790-29049614	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1056726	chr18:28978180-29049614	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1061071	chr18:28979237-29048429	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
22	nsv909518	chr18:29009409-29049018	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29024800-29027600	Weak transcription	Esophagus	oesophagus
2	chr18:29027000-29027600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr18:29027200-29027600	Flanking Active TSS	HMEC	breast
4	chr18:29027200-29030400	Active TSS	Duodenum Mucosa	Duodenum
5	chr18:29027400-29027600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr18:29027400-29027800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr18:29027400-29029200	Active TSS	NHEK	skin
8	chr18:29027400-29030200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr18:29027400-29030800	Active TSS	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links