Variant report

Variant	rs9840958
Chromosome Location	chr3:54014287-54014288
allele	A/C
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:10)

rs_ID	r²[population]
rs28385736	1.00[AMR][1000 genomes]
rs58017417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58865590	1.00[AMR][1000 genomes]
rs59371642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72974943	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72974969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72974972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9814162	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9814454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869398	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1005411	chr3:53927782-54158638	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	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
6	nsv523473	chr3:54010039-54033865	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54012800-54016000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:54013000-54014400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:54013000-54014400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:54013000-54014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:54013200-54014400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:54014000-54015600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:54014200-54014400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:54014200-54015600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:54014200-54015600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:54014200-54019400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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

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