Variant report

Variant	rs630879
Chromosome Location	chr1:241805750-241805751
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs2784165	0.92[AFR][1000 genomes]
rs595397	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs598292	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs610693	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs613797	0.95[AFR][1000 genomes]
rs615141	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs616020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs626437	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs626443	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs629088	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs643321	0.99[AFR][1000 genomes];1.00[AMR][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	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241803800-241806200	Flanking Active TSS	Hela-S3	cervix
2	chr1:241804000-241806200	Flanking Active TSS	A549	lung
3	chr1:241804200-241805800	Enhancers	Placenta	Placenta
4	chr1:241804200-241805800	Enhancers	NHEK	skin
5	chr1:241804200-241806800	Enhancers	Fetal Intestine Large	intestine
6	chr1:241804200-241808600	Weak transcription	Ovary	ovary
7	chr1:241804200-241809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:241804400-241805800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:241804400-241809400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:241804400-241809600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:241804800-241808600	Weak transcription	Gastric	stomach
12	chr1:241805000-241813600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:241805200-241806200	Enhancers	Liver	Liver
14	chr1:241805400-241805800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:241805400-241809400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:241805600-241806200	Enhancers	HepG2	liver
17	chr1:241805600-241810800	Weak transcription	Muscle Satellite Cultured Cells	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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