Variant report

Variant	rs10058476
Chromosome Location	chr5:96297527-96297528
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96270007..96273203-chr5:96295277..96299165,4	K562	blood:
2	chr5:96267069..96273023-chr5:96293959..96302488,9	K562	blood:
3	chr5:96292270..96294978-chr5:96295616..96298359,2	K562	blood:
4	chr5:96293790..96295520-chr5:96295788..96298658,2	K562	blood:
5	chr5:96142628..96144259-chr5:96295095..96298052,3	MCF-7	breast:
6	chr5:96270424..96272050-chr5:96295568..96297957,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164307	Chromatin interaction
ENSG00000113441	Chromatin interaction
ENSG00000247121	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10038651	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10044354	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10051637	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10077945	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10434709	0.85[CEU][hapmap]
rs1046395	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1046396	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10476696	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11135484	0.85[CEU][hapmap]
rs1216566	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1216567	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1216571	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12516666	0.85[CEU][hapmap]
rs13167902	0.85[CEU][hapmap]
rs13170029	0.87[EUR][1000 genomes]
rs13358339	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1363907	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1363908	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1363974	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1363976	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1423357	0.89[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1423566	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1477364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1544777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1559355	0.85[CEU][hapmap]
rs1820148	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1974871	0.88[CEU][hapmap]
rs2113050	0.80[CEU][hapmap]
rs2161548	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2247650	0.82[CEU][hapmap]
rs2278018	0.85[CEU][hapmap]
rs2278019	0.85[CEU][hapmap]
rs2351010	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2351011	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2432141	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs251339	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.80[ASN][1000 genomes]
rs251340	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs251341	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2548224	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2548226	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2548516	0.84[EUR][1000 genomes]
rs2548529	0.89[CHB][hapmap]
rs2548530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2548532	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2549783	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs2549784	0.83[YRI][hapmap]
rs2549794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2617439	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2617447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27289	0.86[EUR][1000 genomes]
rs27290	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs27293	0.86[EUR][1000 genomes]
rs27295	0.86[EUR][1000 genomes]
rs27298	0.82[EUR][1000 genomes]
rs27300	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs27306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs27307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs27436	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2762	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs27659	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs27660	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27993	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]
rs27998	0.82[EUR][1000 genomes]
rs2859491	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2910686	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2910687	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910788	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2910789	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2910793	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2927609	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734015	0.85[CEU][hapmap]
rs3797796	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs38029	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38031	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38032	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38033	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs38034	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs38038	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs38039	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38042	0.82[CEU][hapmap]
rs38043	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs38044	0.87[EUR][1000 genomes]
rs3849749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3909451	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39602	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4360063	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869314	0.85[CEU][hapmap]
rs6556942	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs6859168	0.87[EUR][1000 genomes]
rs6871162	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6887500	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs716848	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7703341	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7705093	0.84[AMR][1000 genomes]
rs7716222	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7719705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7726445	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7731592	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7733312	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9127	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs9314181	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
rs10058476	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs10058476	AC008865.1	cis	Artery Tibial	GTEx
rs10058476	LRAP	cis	lesional skin	skin_eQTL
rs10058476	ERAP2	cis	Artery Tibial	GTEx
rs10058476	ERAP2	cis	Artery Aorta	GTEx
rs10058476	ERAP2	cis	Heart Left Ventricle	GTEx
rs10058476	ERAP2	cis	Thyroid	GTEx
rs10058476	ERAP2	cis	Esophagus Muscularis	GTEx
rs10058476	ERAP2	cis	Esophagus Mucosa	GTEx
rs10058476	ERAP2	cis	Adipose Subcutaneous	GTEx
rs10058476	ERAP2	cis	Whole Blood	GTEx
rs10058476	ERAP2	cis	lung	GTEx
rs10058476	LRAP	cis	uninvolved skin	skin_eQTL
rs10058476	ERAP2	cis	Muscle Skeletal	GTEx
rs10058476	ERAP2	cis	Stomach	GTEx
rs10058476	ERAP2	cis	Nerve Tibial	GTEx
rs10058476	LRAP	cis	normal skin	skin_eQTL
rs10058476	LNPEP	cis	Esophagus Muscularis	GTEx
rs10058476	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96273000-96299200	Weak transcription	Aorta	Aorta
2	chr5:96274600-96298400	Weak transcription	HSMM	muscle
3	chr5:96277800-96303800	Weak transcription	Pancreas	Pancrea
4	chr5:96278200-96314400	Weak transcription	Fetal Intestine Large	intestine
5	chr5:96279800-96298400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:96279800-96303800	Weak transcription	Esophagus	oesophagus
7	chr5:96282200-96303800	Weak transcription	Spleen	Spleen
8	chr5:96285400-96304400	Weak transcription	Fetal Intestine Small	intestine
9	chr5:96286400-96303800	Weak transcription	Right Ventricle	heart
10	chr5:96288400-96303800	Weak transcription	Fetal Stomach	stomach
11	chr5:96289000-96297600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:96289000-96297800	Weak transcription	Right Atrium	heart
13	chr5:96289000-96298800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:96289800-96297600	Weak transcription	HMEC	breast
15	chr5:96289800-96297800	Weak transcription	Stomach Mucosa	stomach
16	chr5:96290000-96297800	Weak transcription	Fetal Kidney	kidney
17	chr5:96290000-96298800	Weak transcription	Fetal Lung	lung
18	chr5:96290200-96298200	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:96290200-96298600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:96290800-96298000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr5:96291200-96297600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr5:96291800-96297800	Weak transcription	HUVEC	blood vessel
23	chr5:96292200-96297800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:96292800-96299400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr5:96292800-96299800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr5:96293200-96298200	Weak transcription	NHLF	lung
27	chr5:96293400-96298600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:96293600-96297800	Weak transcription	K562	blood
29	chr5:96293800-96297800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:96293800-96297800	Weak transcription	Small Intestine	intestine
31	chr5:96293800-96298400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr5:96293800-96299000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:96294000-96303400	Weak transcription	A549	lung
34	chr5:96294400-96297600	Weak transcription	Brain Anterior Caudate	brain
35	chr5:96294400-96297800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:96294400-96297800	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:96294400-96297800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:96294400-96299200	Weak transcription	Liver	Liver
39	chr5:96294600-96299000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:96294600-96303600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:96294800-96297600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:96294800-96297800	Weak transcription	Left Ventricle	heart
43	chr5:96295000-96297800	Weak transcription	Psoas Muscle	Psoas
44	chr5:96295200-96298200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr5:96295800-96302200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:96296000-96298200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:96296000-96299400	Enhancers	NHEK	skin
48	chr5:96296200-96299600	Enhancers	Osteobl	bone
49	chr5:96296400-96297600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:96296400-96297600	Weak transcription	Duodenum Mucosa	Duodenum

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