Variant report

Variant	rs1389099
Chromosome Location	chr4:142692241-142692242
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10003233	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10018460	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10519610	0.86[JPT][hapmap]
rs10833	0.96[CEU][hapmap];0.84[MKK][hapmap]
rs12498901	0.86[JPT][hapmap]
rs12504148	0.86[JPT][hapmap]
rs12510514	0.86[JPT][hapmap]
rs1493015	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607595	0.86[JPT][hapmap]
rs17364630	0.86[JPT][hapmap]
rs1907948	0.91[ASN][1000 genomes]
rs1987968	0.91[ASN][1000 genomes]
rs28504216	0.91[ASN][1000 genomes]
rs28528751	0.88[ASN][1000 genomes]
rs4956405	0.86[JPT][hapmap]
rs6537073	0.89[ASN][1000 genomes]
rs6842735	0.86[JPT][hapmap]
rs6850492	0.86[JPT][hapmap]
rs7349640	0.86[JPT][hapmap]
rs7668411	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7671458	0.86[JPT][hapmap]
rs7694632	0.90[AMR][1000 genomes];0.93[EUR][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	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3448093	chr4:142612197-142704695	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1389099	IL15	cis	multi-tissue	Pritchard
rs1389099	INPP4B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142690000-142693000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:142690400-142692800	Enhancers	A549	lung
3	chr4:142690600-142693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:142690800-142693000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:142690800-142693000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:142690800-142693200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:142690800-142693200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:142691000-142693000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:142691000-142693000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:142691000-142693000	Weak transcription	Osteobl	bone
11	chr4:142691000-142693600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:142692000-142692800	Enhancers	GM12878-XiMat	blood
13	chr4:142692200-142692800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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