Variant report

Variant	rs9849660
Chromosome Location	chr3:54343604-54343605
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11130416	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11130417	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4928040	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6445645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445648	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6784315	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6810202	0.91[EUR][1000 genomes]
rs7427630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7431577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7434239	0.92[EUR][1000 genomes]
rs7618315	0.90[EUR][1000 genomes]
rs7627905	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7632823	0.81[CHB][hapmap]
rs7634811	0.91[EUR][1000 genomes]
rs7652209	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9683195	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9863855	0.94[CEU][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9879885	1.00[CEU][hapmap];0.95[EUR][1000 genomes]

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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54338400-54345400	Weak transcription	Fetal Lung	lung
2	chr3:54343200-54344000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:54343200-54344200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:54343600-54344000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr3:54343600-54344000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:54343600-54344000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:54343600-54344000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:54343600-54344000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:54343600-54344000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:54343600-54344000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:54343600-54344000	Enhancers	Fetal Muscle Leg	muscle
12	chr3:54343600-54344000	Enhancers	Psoas Muscle	Psoas
13	chr3:54343600-54344200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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