Variant report

Variant	rs3795020
Chromosome Location	chr19:42262891-42262892
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11669653	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459454	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1549960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805223	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3795018	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803507	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57827663	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3430577	chr19:42247653-42285973	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv911774	chr19:42250325-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3384883	chr19:42253458-42288853	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3319044	chr19:42257039-42297123	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3319045	chr19:42257039-42297123	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2763205	chr19:42258547-42290598	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv911775	chr19:42259228-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3795020	SLC1A5	cis	parietal	SCAN
rs3795020	SIGLEC11	cis	parietal	SCAN
rs3795020	FUT2	cis	cerebellum	SCAN
rs3795020	SNORD35A	cis	parietal	SCAN
rs3795020	DBP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42259200-42263000	Active TSS	Esophagus	oesophagus
2	chr19:42261000-42263000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr19:42261800-42263200	Enhancers	Primary hematopoietic stem cells	blood
4	chr19:42262000-42266600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr19:42262400-42263600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:42262600-42263000	Flanking Active TSS	Lung	lung
7	chr19:42262600-42263400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr19:42262600-42263600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:42262600-42270400	Weak transcription	Fetal Intestine Small	intestine
10	chr19:42262800-42265200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:42262800-42276600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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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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