Variant report

Variant	rs26489
Chromosome Location	chr5:96133427-96133428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:96130367-96133704	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96130627..96133603-chr5:96137872..96139471,2	K562	blood:
2	chr5:96125568..96129168-chr5:96132966..96137339,5	K562	blood:
3	chr5:96131348..96135034-chr5:96141862..96144719,4	MCF-7	breast:

Variant related genes	Relation type
ERAP1	TF binding region
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs149189	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151823	0.81[ASN][1000 genomes]
rs151940	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151964	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs152280	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs152466	0.81[ASN][1000 genomes]
rs187387	0.81[ASN][1000 genomes]
rs190298	0.81[ASN][1000 genomes]
rs246453	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs246454	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs246455	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs26490	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26491	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26493	0.81[ASN][1000 genomes]
rs26495	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26497	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26498	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26499	0.83[AFR][1000 genomes]
rs26500	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26510	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs26512	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26653	0.89[ASN][1000 genomes]
rs26654	0.89[ASN][1000 genomes]
rs26655	0.89[ASN][1000 genomes]
rs27043	0.83[ASN][1000 genomes]
rs27044	0.83[ASN][1000 genomes]
rs27045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27432	0.84[ASN][1000 genomes]
rs27434	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27527	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs27529	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs27640	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27645	0.81[ASN][1000 genomes]
rs27710	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28119	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28333	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28337	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30185	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30186	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30187	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs30334	0.87[ASN][1000 genomes]
rs30376	0.83[ASN][1000 genomes]
rs30378	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs30379	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs30380	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34737	0.81[ASN][1000 genomes]
rs34750	0.87[ASN][1000 genomes]
rs34751	0.88[ASN][1000 genomes]
rs34752	0.87[ASN][1000 genomes]
rs39840	0.83[ASN][1000 genomes]
rs39841	0.82[ASN][1000 genomes]
rs42398	0.83[ASN][1000 genomes]
rs467735	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469367	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs469674	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs469758	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs469783	0.95[ASN][1000 genomes]
rs695965	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	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
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs26489	ERAP1	cis	Whole Blood	GTEx
rs26489	ERAP1	cis	Nerve Tibial	GTEx
rs26489	ERAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs26489	ERAP1	cis	lung	GTEx
rs26489	ERAP1	cis	Esophagus Mucosa	GTEx
rs26489	CTD-2260A17.1	cis	Whole Blood	GTEx
rs26489	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs26489	ERAP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
5	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
6	chr5:96104200-96136400	Strong transcription	Dnd41	blood
7	chr5:96107800-96138200	Strong transcription	GM12878-XiMat	blood
8	chr5:96113800-96137200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:96115200-96141200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:96115400-96142000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:96116200-96141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:96117400-96137000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr5:96119000-96142000	Weak transcription	A549	lung
14	chr5:96123600-96137000	Strong transcription	Primary B cells from cord blood	blood
15	chr5:96123800-96137200	Strong transcription	Adipose Nuclei	Adipose
16	chr5:96124600-96136800	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:96126800-96135600	Weak transcription	Fetal Heart	heart
18	chr5:96126800-96142800	Weak transcription	Brain Germinal Matrix	brain
19	chr5:96127000-96135400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:96127000-96140400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:96127000-96142600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:96127000-96142800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:96127200-96137000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:96127200-96137000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr5:96127200-96137400	Strong transcription	Placenta	Placenta
26	chr5:96127200-96139600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:96127200-96139800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:96127400-96135800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr5:96127400-96136800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr5:96127400-96142600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:96127400-96142600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr5:96127400-96142600	Weak transcription	NH-A	brain
33	chr5:96127600-96133600	Strong transcription	NHEK	skin
34	chr5:96127600-96136200	Strong transcription	Fetal Intestine Large	intestine
35	chr5:96127600-96141600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:96127600-96142800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:96128400-96137400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:96128800-96137200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:96129000-96133600	Strong transcription	Colon Smooth Muscle	Colon
40	chr5:96129000-96137000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr5:96129000-96137400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:96129400-96136000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:96129400-96137200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:96129400-96137200	Strong transcription	Lung	lung
45	chr5:96129400-96137400	Strong transcription	Left Ventricle	heart
46	chr5:96129600-96133600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:96129600-96133800	Strong transcription	Brain Hippocampus Middle	brain
48	chr5:96129600-96133800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr5:96129600-96135600	Strong transcription	Brain Cingulate Gyrus	brain
50	chr5:96129600-96136800	Strong transcription	Brain Anterior Caudate	brain

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