Variant report

Variant	rs2289739
Chromosome Location	chr15:41801512-41801513
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1077809	0.87[GIH][hapmap]
rs11070332	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2253936	0.87[GIH][hapmap]
rs2297379	0.90[ASW][hapmap]
rs2412620	0.86[YRI][hapmap]
rs2777490	0.82[ASW][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs316622	0.82[ASW][hapmap]
rs316623	0.82[ASW][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs3759793	0.87[GIH][hapmap]

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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats 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	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv569233	chr15:41784809-41805237	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv33378	chr15:41786505-41805760	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2289739	LTK	cis	lung	GTEx
rs2289739	RPAP1	cis	multi-tissue	Pritchard
rs2289739	TYRO3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41789400-41802600	Weak transcription	K562	blood
2	chr15:41795400-41803600	Weak transcription	Lung	lung
3	chr15:41795400-41804200	Weak transcription	Right Atrium	heart
4	chr15:41798200-41803000	Weak transcription	Spleen	Spleen
5	chr15:41798800-41801600	Enhancers	Stomach Mucosa	stomach
6	chr15:41799000-41801600	Enhancers	Duodenum Mucosa	Duodenum
7	chr15:41800400-41803400	Weak transcription	Gastric	stomach
8	chr15:41800800-41801600	Flanking Active TSS	Hela-S3	cervix
9	chr15:41801200-41802400	Weak transcription	Fetal Intestine Small	intestine
10	chr15:41801200-41803600	Weak transcription	Pancreas	Pancrea
11	chr15:41801400-41802800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:41801400-41803000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:41801400-41803200	Weak transcription	Colonic Mucosa	Colon

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

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