Variant report

Variant	rs12659825
Chromosome Location	chr5:96188083-96188084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96187112..96188825-chr5:96189187..96193185,3	MCF-7	breast:
2	chr5:96188005..96191369-chr5:96193266..96198174,6	K562	blood:
3	chr5:96184835..96188350-chr5:96188739..96192448,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1230366	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519842	1.00[ASN][1000 genomes]
rs12659038	0.84[ASN][1000 genomes]
rs151823	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs151908	0.92[YRI][hapmap]
rs151911	0.90[YRI][hapmap]
rs151940	0.87[CHB][hapmap]
rs151953	0.92[YRI][hapmap]
rs152280	1.00[YRI][hapmap]
rs152468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs184971	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs2042381	0.97[ASN][1000 genomes]
rs2351012	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351013	1.00[ASN][1000 genomes]
rs245472	0.98[ASN][1000 genomes]
rs246453	0.87[CHB][hapmap]
rs249960	0.97[ASN][1000 genomes]
rs2545629	0.98[ASN][1000 genomes]
rs2549804	1.00[ASN][1000 genomes]
rs2549805	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs26491	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs26493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26495	0.87[CHB][hapmap]
rs26496	0.87[CHB][hapmap]
rs26498	0.87[CHB][hapmap]
rs26510	0.87[CHB][hapmap]
rs26654	0.82[CHB][hapmap]
rs27043	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs27044	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs27045	0.87[CHB][hapmap]
rs27432	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs27434	0.86[CHB][hapmap]
rs27527	0.87[YRI][hapmap]
rs27529	0.87[CHB][hapmap]
rs27694	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs27710	0.87[CHB][hapmap]
rs28119	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs28129	0.92[YRI][hapmap]
rs2911138	0.97[ASN][1000 genomes]
rs2911139	0.97[ASN][1000 genomes]
rs2927619	1.00[ASN][1000 genomes]
rs2927620	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30186	0.87[CHB][hapmap]
rs30187	0.87[CHB][hapmap]
rs30376	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs30378	0.91[CHB][hapmap]
rs30379	0.87[CHB][hapmap]
rs30380	0.87[CHB][hapmap]
rs34735	1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs34753	0.89[YRI][hapmap]
rs34756	0.89[YRI][hapmap]
rs34761	0.85[YRI][hapmap]
rs39840	0.84[ASN][1000 genomes]
rs39841	0.84[ASN][1000 genomes]
rs3985002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40604	0.95[YRI][hapmap]
rs42398	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs468130	0.92[YRI][hapmap]
rs469758	0.91[CHB][hapmap]
rs469783	0.83[CHB][hapmap]
rs4869315	0.86[JPT][hapmap]
rs61112531	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709668	0.99[ASN][1000 genomes]
rs845028	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv432756	chr5:96113844-96234644	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12659825	ERAP1	cis	lung	GTEx
rs12659825	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs12659825	ERAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12659825	ERAP1	cis	Whole Blood	GTEx
rs12659825	CTD-2260A17.3	cis	Whole Blood	GTEx
rs12659825	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs12659825	CTD-2260A17.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96186800-96188800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:96187000-96190800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:96187200-96190200	Enhancers	NHDF-Ad	bronchial
4	chr5:96187400-96188200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:96187400-96188400	Weak transcription	Osteobl	bone
6	chr5:96187400-96190200	Weak transcription	NHLF	lung
7	chr5:96187600-96188200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:96187800-96188800	Weak transcription	Adipose Nuclei	Adipose
9	chr5:96188000-96188400	Enhancers	Fetal Brain Male	brain
10	chr5:96188000-96189000	Enhancers	NH-A	brain

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