Variant report

Variant	rs2549783
Chromosome Location	chr5:96231372-96231373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10038651	0.85[EUR][1000 genomes]
rs10044354	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs10051637	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10058476	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs10077945	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10434709	0.85[CEU][hapmap]
rs1046395	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1046396	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10476696	0.85[EUR][1000 genomes]
rs11135484	0.85[CEU][hapmap]
rs1216566	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1216567	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1216571	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12516666	0.86[CEU][hapmap]
rs13167902	0.85[CEU][hapmap]
rs13170029	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13358339	0.85[EUR][1000 genomes]
rs1363907	0.96[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1363908	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1363974	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1363976	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1423357	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1423566	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1477364	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1544777	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes]
rs1559355	0.86[CEU][hapmap]
rs1820148	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1974871	0.89[CEU][hapmap];0.88[YRI][hapmap]
rs2113050	0.80[CEU][hapmap]
rs2161548	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2247650	0.82[CEU][hapmap]
rs2278018	0.85[CEU][hapmap]
rs2278019	0.85[CEU][hapmap]
rs2351010	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2351011	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2432141	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2432142	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs251339	0.82[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs251340	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs251341	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs251343	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2548224	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548226	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548516	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2548527	0.82[YRI][hapmap]
rs2548530	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2548532	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2549784	0.92[YRI][hapmap]
rs2549794	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2617435	0.80[EUR][1000 genomes]
rs2617439	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2617447	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs27289	0.83[EUR][1000 genomes]
rs27290	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs27293	0.83[EUR][1000 genomes]
rs27295	0.83[EUR][1000 genomes]
rs27300	0.89[CEU][hapmap]
rs27306	1.00[CEU][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes]
rs27307	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs27436	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2762	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs27659	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs27660	0.88[EUR][1000 genomes]
rs27711	1.00[CEU][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes]
rs27712	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs27993	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2859491	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2910686	0.86[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2910687	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2910788	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2910789	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2910793	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2927608	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2927609	1.00[CEU][hapmap];0.80[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3734015	0.86[CEU][hapmap]
rs3797796	0.96[CEU][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs38029	0.88[EUR][1000 genomes]
rs38031	0.88[EUR][1000 genomes]
rs38032	0.96[CEU][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs38033	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs38034	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs38038	0.83[EUR][1000 genomes]
rs38039	0.88[EUR][1000 genomes]
rs38042	0.82[CEU][hapmap]
rs38043	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs38044	0.83[EUR][1000 genomes]
rs3849749	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3909451	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs39602	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs4360063	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs4869313	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4869314	0.86[CEU][hapmap]
rs55770741	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6556942	0.96[CEU][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6859168	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6871162	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6873866	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6887500	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs716848	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7703341	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7716222	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7719705	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7726445	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7731592	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7733312	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9127	0.92[CEU][hapmap]
rs9314181	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2549783	LRAP	cis	normal skin	skin_eQTL
rs2549783	ERAP2	cis	Stomach	GTEx
rs2549783	ERAP2	cis	Esophagus Mucosa	GTEx
rs2549783	LRAP	cis	uninvolved skin	skin_eQTL
rs2549783	ERAP2	cis	Adipose Subcutaneous	GTEx
rs2549783	ERAP2	cis	Muscle Skeletal	GTEx
rs2549783	ERAP2	cis	Nerve Tibial	GTEx
rs2549783	ERAP2	cis	Esophagus Muscularis	GTEx
rs2549783	ERAP2	cis	Artery Tibial	GTEx
rs2549783	LNPEP	cis	Esophagus Muscularis	GTEx
rs2549783	ERAP2	cis	Heart Left Ventricle	GTEx
rs2549783	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs2549783	ERAP2	cis	Thyroid	GTEx
rs2549783	LRAP	cis	lesional skin	skin_eQTL
rs2549783	ERAP2	cis	lung	GTEx
rs2549783	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs2549783	ERAP2	cis	Whole Blood	GTEx
rs2549783	ERAP2	cis	Artery Aorta	GTEx
rs2549783	AC008865.1	cis	Artery Tibial	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96212600-96232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:96213000-96239000	Weak transcription	Pancreas	Pancrea
3	chr5:96213400-96237800	Weak transcription	Brain Substantia Nigra	brain
4	chr5:96213400-96243800	Weak transcription	HepG2	liver
5	chr5:96213400-96247000	Weak transcription	Fetal Lung	lung
6	chr5:96217600-96241600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:96217600-96250000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:96217800-96237800	Weak transcription	NHDF-Ad	bronchial
9	chr5:96218000-96237000	Weak transcription	NHLF	lung
10	chr5:96218000-96264600	Weak transcription	Right Ventricle	heart
11	chr5:96218200-96231400	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:96218200-96232000	Weak transcription	Brain Anterior Caudate	brain
13	chr5:96218200-96237000	Weak transcription	Hela-S3	cervix
14	chr5:96218600-96259600	Weak transcription	HMEC	breast
15	chr5:96221000-96236600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:96221600-96269200	Weak transcription	Fetal Brain Male	brain
17	chr5:96221800-96235600	Weak transcription	Right Atrium	heart
18	chr5:96221800-96242200	Strong transcription	Dnd41	blood
19	chr5:96222000-96268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:96222400-96231800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:96222400-96242600	Strong transcription	Fetal Thymus	thymus
22	chr5:96222400-96247200	Weak transcription	Psoas Muscle	Psoas
23	chr5:96222400-96258200	Weak transcription	Stomach Mucosa	stomach
24	chr5:96222600-96232000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:96223200-96240400	Strong transcription	Liver	Liver
26	chr5:96223400-96231600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr5:96223600-96231400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:96223600-96231400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:96223600-96240600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr5:96224000-96231600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr5:96224800-96231400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr5:96225200-96244600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:96225600-96235800	Weak transcription	Lung	lung
34	chr5:96225600-96236600	Weak transcription	Spleen	Spleen
35	chr5:96225600-96245200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:96225600-96266400	Weak transcription	Gastric	stomach
37	chr5:96226200-96244000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:96226400-96237000	Weak transcription	Placenta	Placenta
39	chr5:96227800-96231800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr5:96227800-96232600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:96228400-96232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr5:96229000-96232400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:96229200-96245400	Weak transcription	HSMMtube	muscle
44	chr5:96229400-96232000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:96229600-96235800	Weak transcription	Ovary	ovary
46	chr5:96229600-96236400	Weak transcription	Fetal Stomach	stomach
47	chr5:96229600-96236600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:96229600-96237000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:96229600-96238600	Weak transcription	HSMM	muscle
50	chr5:96229600-96238800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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