Variant report

Variant	rs3001288
Chromosome Location	chr1:159926436-159926437
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11591079	1.00[CHB][hapmap]
rs1320570	1.00[CHB][hapmap]
rs17427209	1.00[CHB][hapmap]
rs17467492	1.00[CHB][hapmap]
rs2789415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789420	0.89[EUR][1000 genomes]
rs2820579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2820584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2840581	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs2840583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2840586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2840588	1.00[CHB][hapmap]
rs4402127	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs6662675	1.00[CHB][hapmap]
rs6662918	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520773	chr1:159922959-159935569	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
2	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:159924000-159927800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:159924000-159928800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:159924000-159928800	Weak transcription	Esophagus	oesophagus
6	chr1:159924200-159928400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:159924400-159927200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:159924400-159927200	Weak transcription	K562	blood
9	chr1:159924400-159929200	Weak transcription	Osteobl	bone
10	chr1:159925200-159929600	Weak transcription	NHDF-Ad	bronchial
11	chr1:159925400-159929000	Weak transcription	HMEC	breast
12	chr1:159925600-159927800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:159926200-159927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:159926400-159927800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:159926400-159928800	Weak transcription	NHEK	skin

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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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