Variant report

Variant	rs27993
Chromosome Location	chr5:96355603-96355604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10038651	0.87[EUR][1000 genomes]
rs10044354	0.89[CEU][hapmap];0.85[CHD][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10051637	0.89[CEU][hapmap];0.85[CHD][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs10058476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10069361	0.85[CHD][hapmap]
rs10077945	0.83[EUR][1000 genomes]
rs10434709	0.85[CEU][hapmap]
rs1046395	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1046396	0.85[EUR][1000 genomes]
rs10476696	0.87[EUR][1000 genomes]
rs11135484	0.85[CEU][hapmap]
rs1216566	0.89[EUR][1000 genomes]
rs1216567	0.89[EUR][1000 genomes]
rs1216571	0.89[EUR][1000 genomes]
rs1230358	0.83[JPT][hapmap];0.93[TSI][hapmap]
rs12516666	0.85[CEU][hapmap]
rs13167902	0.85[CEU][hapmap]
rs13170029	0.85[EUR][1000 genomes]
rs13358339	0.87[EUR][1000 genomes]
rs1363907	0.93[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1363908	0.88[EUR][1000 genomes]
rs1363974	0.89[CEU][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1363976	0.86[EUR][1000 genomes]
rs1423357	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1423566	0.85[EUR][1000 genomes]
rs1477364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1544777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1559355	0.85[CEU][hapmap]
rs18059	0.83[CHD][hapmap]
rs1820148	0.88[EUR][1000 genomes]
rs1974871	0.89[CEU][hapmap]
rs2161548	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2247650	0.82[CEU][hapmap]
rs2278018	0.85[CEU][hapmap]
rs2278019	0.85[CEU][hapmap]
rs2351010	0.89[CEU][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2351011	0.88[EUR][1000 genomes]
rs2432141	0.84[EUR][1000 genomes]
rs251339	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs251340	0.88[EUR][1000 genomes]
rs251341	0.87[EUR][1000 genomes]
rs2548224	0.82[EUR][1000 genomes]
rs2548226	0.84[EUR][1000 genomes]
rs2548516	0.82[EUR][1000 genomes]
rs2548527	0.82[ASW][hapmap]
rs2548529	0.89[CHB][hapmap]
rs2548530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2548532	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2549778	0.83[JPT][hapmap];0.93[TSI][hapmap]
rs2549783	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2549794	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2617438	0.83[JPT][hapmap]
rs2617439	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2617447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes]
rs27289	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27290	0.89[CEU][hapmap];0.83[CHD][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27293	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27294	0.80[EUR][1000 genomes]
rs27295	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27298	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs27300	0.89[CEU][hapmap];0.85[CHD][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs27302	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs27306	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27436	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs27613	0.85[CHD][hapmap]
rs2762	0.81[CEU][hapmap];0.85[CHD][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs27659	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs27660	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27998	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2859491	0.88[EUR][1000 genomes]
rs2910686	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2910687	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2910787	0.85[CHD][hapmap]
rs2910788	0.85[EUR][1000 genomes]
rs2910789	0.85[EUR][1000 genomes]
rs2910793	0.88[EUR][1000 genomes]
rs2927609	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs31398	0.80[EUR][1000 genomes]
rs3734015	0.85[CEU][hapmap]
rs3797796	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs38029	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38030	0.80[EUR][1000 genomes]
rs38031	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38032	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38033	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs38034	0.85[CEU][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs38038	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38039	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38040	0.85[CHD][hapmap]
rs38042	0.82[CEU][hapmap]
rs38043	0.89[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38044	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3849749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs3909451	0.89[CEU][hapmap];0.83[CHD][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs39602	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4360063	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs4869314	0.85[CEU][hapmap]
rs6556942	0.96[CEU][hapmap];0.94[JPT][hapmap]
rs6859168	0.86[EUR][1000 genomes]
rs6871162	0.89[CEU][hapmap];0.85[CHD][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs6887500	0.85[EUR][1000 genomes]
rs716848	0.89[EUR][1000 genomes]
rs7703341	0.85[EUR][1000 genomes]
rs7716222	0.89[CEU][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7719705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726445	0.85[EUR][1000 genomes]
rs7731592	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7733312	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9127	0.92[CEU][hapmap]
rs9314181	0.87[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	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	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
5	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
6	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

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs27993	LNPEP	cis	Esophagus Muscularis	GTEx
rs27993	ERAP2	cis	Artery Aorta	GTEx
rs27993	ARTS-1	cis	multi-tissue	Pritchard
rs27993	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs27993	ERAP2	cis	Esophagus Muscularis	GTEx
rs27993	LRAP	cis	lesional skin	skin_eQTL
rs27993	LNPEP	cis	Artery Tibial	GTEx
rs27993	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs27993	ERAP2	cis	lung	GTEx
rs27993	ERAP2	cis	Stomach	GTEx
rs27993	ERAP2	cis	Thyroid	GTEx
rs27993	ERAP2	cis	Heart Left Ventricle	GTEx
rs27993	ERAP2	cis	Artery Tibial	GTEx
rs27993	LNPEP	trans	brain	seeQTL
rs27993	LRAP	cis	uninvolved skin	skin_eQTL
rs27993	LNPEP	cis	brain	seeQTL
rs27993	LRAP	cis	normal skin	skin_eQTL
rs27993	ERAP2	cis	Nerve Tibial	GTEx
rs27993	ERAP2	cis	Esophagus Mucosa	GTEx
rs27993	ERAP2	cis	Adipose Subcutaneous	GTEx
rs27993	AC008865.1	cis	Artery Tibial	GTEx
rs27993	LRAP	cis	multi-tissue	Pritchard
rs27993	ERAP2	cis	Muscle Skeletal	GTEx
rs27993	ERAP2	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96304800-96359600	Weak transcription	Hela-S3	cervix
2	chr5:96314000-96360200	Weak transcription	Fetal Brain Male	brain
3	chr5:96315400-96374800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:96315600-96358600	Weak transcription	Brain Substantia Nigra	brain
5	chr5:96316000-96360000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:96320000-96357600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:96322400-96358600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:96322400-96359600	Weak transcription	Gastric	stomach
9	chr5:96329800-96358800	Weak transcription	Brain Germinal Matrix	brain
10	chr5:96330000-96359800	Weak transcription	Aorta	Aorta
11	chr5:96330400-96359400	Weak transcription	Fetal Brain Female	brain
12	chr5:96331600-96356200	Weak transcription	Fetal Stomach	stomach
13	chr5:96331600-96357800	Weak transcription	Spleen	Spleen
14	chr5:96333600-96374000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:96333800-96372800	Strong transcription	Placenta	Placenta
16	chr5:96335800-96359600	Weak transcription	Stomach Mucosa	stomach
17	chr5:96336200-96357800	Weak transcription	Fetal Intestine Small	intestine
18	chr5:96336600-96359400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:96336600-96359400	Weak transcription	Colonic Mucosa	Colon
20	chr5:96340600-96359800	Weak transcription	NHDF-Ad	bronchial
21	chr5:96340800-96359800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:96341000-96358800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:96342600-96374400	Weak transcription	HepG2	liver
24	chr5:96342800-96358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:96343000-96359000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:96343200-96355800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:96343200-96360000	Weak transcription	Brain Angular Gyrus	brain
28	chr5:96344800-96356000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:96344800-96356200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr5:96345400-96357800	Strong transcription	Dnd41	blood
31	chr5:96345600-96358800	Weak transcription	Small Intestine	intestine
32	chr5:96345800-96357600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:96345800-96359600	Weak transcription	K562	blood
34	chr5:96346000-96357600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:96346400-96356800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:96346400-96357400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:96346600-96356200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:96346600-96356600	Strong transcription	Primary T cells from cord blood	blood
39	chr5:96346600-96356800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:96346600-96357000	Strong transcription	Adipose Nuclei	Adipose
41	chr5:96346600-96357200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr5:96346600-96358600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:96346600-96372600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr5:96346800-96356200	Strong transcription	Primary B cells from cord blood	blood
45	chr5:96346800-96357200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:96346800-96357800	Strong transcription	GM12878-XiMat	blood
47	chr5:96347000-96373600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr5:96347200-96360400	Weak transcription	Lung	lung
49	chr5:96347200-96363400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr5:96348200-96356800	Strong transcription	Primary neutrophils fromperipheralblood	blood

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