Variant report

Variant	rs6551411
Chromosome Location	chr3:89454900-89454901
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11923388	0.86[YRI][hapmap]
rs1512184	1.00[AMR][1000 genomes]
rs60080797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6763738	1.00[ASW][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6782737	1.00[AMR][1000 genomes]
rs6798377	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923609	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923612	1.00[AMR][1000 genomes]
rs72923614	1.00[AMR][1000 genomes]
rs7636790	1.00[ASW][hapmap];0.87[MKK][hapmap];0.81[YRI][hapmap];0.83[AMR][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	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	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	chr3:89436600-89461800	Weak transcription	Fetal Brain Female	brain
2	chr3:89454000-89455000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:89454400-89455000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:89454400-89455000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:89454400-89455000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:89454400-89455000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:89454400-89455600	Enhancers	Fetal Lung	lung
8	chr3:89454400-89459800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:89454600-89460200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:89454800-89456400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:89454800-89456800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:89454800-89456800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:89454800-89458200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:89454800-89458800	Weak transcription	Fetal Stomach	stomach
15	chr3:89454800-89460200	Weak transcription	H1 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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