Variant report

Variant	rs55642098
Chromosome Location	chr1:242156252-242156253
allele	C/T
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	USF2	chr1:242156166-242156253	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr1:242156018-242156308	Hela-S3	cervix:	n/a	n/a
3	FOS	chr1:242156021-242156384	MCF10A-Er-Src	breast:	n/a	n/a
4	JUND	chr1:242156006-242156395	Hela-S3	cervix:	n/a	chr1:242156205-242156216
5	JUND	chr1:242156112-242156312	HepG2	liver:	n/a	chr1:242156205-242156216
6	CHD2	chr1:242156098-242156339	Hela-S3	cervix:	n/a	n/a
7	MYC	chr1:242156127-242156280	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:242156071-242156333	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:242156000-242156379	Hela-S3	cervix:	n/a	n/a
10	FOS	chr1:242155994-242156385	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:242156021-242156389	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr1:242156009-242156368	Hela-S3	cervix:	n/a	n/a
13	FOS	chr1:242156022-242156383	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr1:242156113-242156350	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CFL1P4	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs2090691	0.91[ASN][1000 genomes]
rs2090692	0.91[ASN][1000 genomes]
rs2102911	0.91[ASN][1000 genomes]
rs28449792	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28477715	0.89[ASN][1000 genomes]
rs28489334	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28507487	0.87[ASN][1000 genomes]
rs28679399	0.87[ASN][1000 genomes]
rs28693018	0.91[ASN][1000 genomes]
rs28699136	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28704168	0.91[ASN][1000 genomes]
rs28707795	0.91[ASN][1000 genomes]
rs34947819	0.91[ASN][1000 genomes]
rs55692832	0.91[ASN][1000 genomes]
rs55823431	0.89[ASN][1000 genomes]
rs56347031	0.89[ASN][1000 genomes]
rs61844958	0.87[ASN][1000 genomes]
rs61844959	0.89[ASN][1000 genomes]
rs61846260	0.89[ASN][1000 genomes]
rs61846264	0.89[ASN][1000 genomes]
rs61846285	0.87[ASN][1000 genomes]
rs61846287	0.91[ASN][1000 genomes]
rs61846299	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61846300	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61846303	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72759104	0.89[ASN][1000 genomes]
rs72759106	0.91[ASN][1000 genomes]
rs72759107	0.91[ASN][1000 genomes]
rs72759108	0.91[ASN][1000 genomes]
rs72759110	0.91[ASN][1000 genomes]
rs72759113	0.91[ASN][1000 genomes]
rs72759115	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1008886	chr1:242015591-242176983	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv2750830	chr1:242025098-242303357	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv2750831	chr1:242025098-242332959	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1002309	chr1:242042242-242295635	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv3353742	chr1:242129501-242179261	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv869647	chr1:242141471-242248271	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv508703	chr1:242146940-242252101	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242121400-242161800	Weak transcription	Right Atrium	heart
2	chr1:242152000-242156600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:242152600-242156600	Weak transcription	Placenta	Placenta
4	chr1:242152600-242161400	Weak transcription	Adipose Nuclei	Adipose
5	chr1:242152600-242161600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:242153600-242158200	Weak transcription	Fetal Lung	lung
7	chr1:242153600-242161000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:242153600-242161400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:242154400-242156800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:242154400-242161000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:242154400-242161600	Weak transcription	Ovary	ovary
12	chr1:242154600-242157000	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:242155200-242157000	Enhancers	Hela-S3	cervix
14	chr1:242155800-242156600	Enhancers	HSMM	muscle
15	chr1:242155800-242156600	Enhancers	NHDF-Ad	bronchial
16	chr1:242155800-242157000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:242156000-242156400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:242156000-242156600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:242156200-242156600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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