Variant report

Variant	rs561258
Chromosome Location	chr1:57589665-57589666
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11206975	1.00[JPT][hapmap]
rs12090414	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408256	1.00[JPT][hapmap]
rs12564278	1.00[JPT][hapmap]
rs12566320	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17115105	1.00[JPT][hapmap]
rs17115108	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17115146	1.00[JPT][hapmap]
rs17115155	1.00[JPT][hapmap]
rs476568	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs484064	0.86[EUR][1000 genomes]
rs490793	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs502701	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506832	0.86[EUR][1000 genomes]
rs510824	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs513259	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs519401	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535415	0.86[EUR][1000 genomes]
rs537307	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs546020	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs549622	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs550511	0.86[EUR][1000 genomes]
rs553453	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs553508	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556204	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs563921	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs564665	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs578962	0.86[EUR][1000 genomes]
rs579057	0.82[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers 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 target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57577200-57595600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57583600-57593000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:57584600-57589800	Weak transcription	NHEK	skin
5	chr1:57585000-57592400	Weak transcription	Fetal Heart	heart
6	chr1:57587200-57590000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:57588200-57596800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:57589200-57591000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:57589400-57608600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:57589600-57590600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:57589600-57591000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:57589600-57592600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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