Variant report

Variant	rs13139573
Chromosome Location	chr4:142616194-142616195
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:142597917..142599701-chr4:142616061..142617565,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1027280	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1027281	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10519613	0.81[CHD][hapmap]
rs1057972	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11100725	0.85[EUR][1000 genomes]
rs11935530	0.85[EUR][1000 genomes]
rs11940083	0.86[EUR][1000 genomes]
rs12508335	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12510030	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13106911	0.83[CHD][hapmap]
rs13112582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13117878	0.96[CEU][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs13122930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13123506	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13126364	0.87[EUR][1000 genomes]
rs13130898	0.85[EUR][1000 genomes]
rs1493022	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1493025	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1602774	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1602775	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17007610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1873822	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030326	0.87[EUR][1000 genomes]
rs2090664	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2139383	0.88[EUR][1000 genomes]
rs2291596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2322300	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2322301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2322302	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2857261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775596	0.81[CHD][hapmap]
rs4104674	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4245934	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4254850	0.81[EUR][1000 genomes]
rs4530709	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597912	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4956405	0.96[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs55849760	0.85[EUR][1000 genomes]
rs6537060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537062	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6537063	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537064	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537070	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6812078	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6819823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831361	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6847434	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852617	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7677372	0.84[EUR][1000 genomes]
rs932209	0.96[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats 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	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
3	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
4	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
5	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
6	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
7	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
rs13139573	IL15	cis	multi-tissue	Pritchard
rs13139573	INPP4B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142583400-142634600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:142601800-142616400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:142602800-142616400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:142608400-142628800	Weak transcription	Aorta	Aorta
5	chr4:142608400-142629000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:142608800-142624200	Weak transcription	Spleen	Spleen
7	chr4:142608800-142655000	Weak transcription	Gastric	stomach
8	chr4:142613400-142628800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:142613400-142629000	Weak transcription	Left Ventricle	heart
10	chr4:142613800-142617200	Weak transcription	Hela-S3	cervix

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