Variant report

Variant	rs1397854
Chromosome Location	chr20:41465048-41465049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12479567	0.86[CEU][hapmap]
rs12480562	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12480719	0.86[CEU][hapmap]
rs12481078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17811383	0.92[CEU][hapmap]
rs206636	1.00[LWK][hapmap]
rs35349846	1.00[ASW][hapmap]
rs4812614	1.00[ASW][hapmap]
rs6093732	0.86[CEU][hapmap]
rs766055	0.86[CEU][hapmap]
rs926479	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41462200-41465600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr20:41464400-41465200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr20:41464400-41466400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr20:41464600-41465600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr20:41464600-41465600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:41464600-41465800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr20:41464800-41465200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr20:41464800-41465400	Enhancers	H9 Cell Line	embryonic stem cell
9	chr20:41464800-41465400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr20:41464800-41466000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:41465000-41465800	Enhancers	Cortex derived primary cultured neurospheres	brain

Quick Search:

Input of quick search could be:

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

what's new

Quick links