Variant report

Variant	rs251342
Chromosome Location	chr5:96236843-96236844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96231747..96233863-chr5:96236335..96237893,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164308	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10061936	0.87[EUR][1000 genomes]
rs10069361	0.91[EUR][1000 genomes]
rs10071975	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10076136	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1019503	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10434708	0.86[ASN][1000 genomes]
rs10434709	0.86[ASN][1000 genomes]
rs10463196	0.82[ASN][1000 genomes]
rs1056893	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11135483	0.86[ASN][1000 genomes]
rs11135484	0.86[ASN][1000 genomes]
rs11135485	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11750025	0.86[ASN][1000 genomes]
rs1216565	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216568	0.87[EUR][1000 genomes]
rs1216569	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216570	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12189125	0.86[ASN][1000 genomes]
rs1230381	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1230382	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12516666	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12654015	0.86[ASN][1000 genomes]
rs12716486	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13163165	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13189819	0.86[ASN][1000 genomes]
rs1363975	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1363977	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1423568	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559267	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1559354	0.86[ASN][1000 genomes]
rs1559355	0.85[ASN][1000 genomes]
rs17087165	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171647	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820149	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187265	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193993	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs193994	0.94[EUR][1000 genomes]
rs1981846	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042383	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042385	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2112974	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2113050	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2113189	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2113190	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113191	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161657	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2161658	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247650	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2248374	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255546	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255633	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255634	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255637	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278018	0.86[ASN][1000 genomes]
rs2278019	0.86[ASN][1000 genomes]
rs2287988	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248215	0.81[EUR][1000 genomes]
rs251339	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs251344	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548520	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548521	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548522	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548523	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548524	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548526	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548527	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548528	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548533	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548534	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548535	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548536	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548537	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548538	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548539	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548540	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549781	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549782	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549784	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549785	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549786	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2549787	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549788	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549789	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549790	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549791	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549792	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549795	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549796	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549797	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549798	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549799	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2549800	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2549801	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617434	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27292	0.85[EUR][1000 genomes]
rs27294	0.83[EUR][1000 genomes]
rs27296	0.81[EUR][1000 genomes]
rs27305	0.85[EUR][1000 genomes]
rs27397	0.85[EUR][1000 genomes]
rs27613	0.83[EUR][1000 genomes]
rs27621	0.81[EUR][1000 genomes]
rs27747	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2910686	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2910688	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2910787	0.91[EUR][1000 genomes]
rs2927608	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3096167	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs31398	0.83[EUR][1000 genomes]
rs33934033	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734015	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38030	0.83[EUR][1000 genomes]
rs38035	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38036	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38037	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38040	0.83[EUR][1000 genomes]
rs38041	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38042	0.85[EUR][1000 genomes]
rs3849750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42983	0.83[EUR][1000 genomes]
rs4869311	0.86[ASN][1000 genomes]
rs4869312	0.86[ASN][1000 genomes]
rs4869313	0.85[ASN][1000 genomes]
rs4869314	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56197090	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6556943	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6859160	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868302	0.86[ASN][1000 genomes]
rs6870825	0.91[EUR][1000 genomes]
rs6873441	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6874656	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6879678	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7700332	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7713127	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7721944	0.86[ASN][1000 genomes]
rs7722694	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7736466	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs251342	ERAP2	cis	Heart Left Ventricle	GTEx
rs251342	ERAP2	cis	Artery Aorta	GTEx
rs251342	ERAP2	cis	Thyroid	GTEx
rs251342	ERAP2	cis	Nerve Tibial	GTEx
rs251342	ERAP2	cis	Artery Tibial	GTEx
rs251342	ERAP2	cis	Muscle Skeletal	GTEx
rs251342	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs251342	ERAP2	cis	Whole Blood	GTEx
rs251342	ERAP2	cis	Stomach	GTEx
rs251342	ERAP2	cis	lung	GTEx
rs251342	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs251342	ERAP2	cis	Adipose Subcutaneous	GTEx
rs251342	ERAP2	cis	Esophagus Muscularis	GTEx
rs251342	ERAP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96213000-96239000	Weak transcription	Pancreas	Pancrea
2	chr5:96213400-96237800	Weak transcription	Brain Substantia Nigra	brain
3	chr5:96213400-96243800	Weak transcription	HepG2	liver
4	chr5:96213400-96247000	Weak transcription	Fetal Lung	lung
5	chr5:96217600-96241600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:96217600-96250000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:96217800-96237800	Weak transcription	NHDF-Ad	bronchial
8	chr5:96218000-96237000	Weak transcription	NHLF	lung
9	chr5:96218000-96264600	Weak transcription	Right Ventricle	heart
10	chr5:96218200-96237000	Weak transcription	Hela-S3	cervix
11	chr5:96218600-96259600	Weak transcription	HMEC	breast
12	chr5:96221600-96269200	Weak transcription	Fetal Brain Male	brain
13	chr5:96221800-96242200	Strong transcription	Dnd41	blood
14	chr5:96222000-96268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:96222400-96242600	Strong transcription	Fetal Thymus	thymus
16	chr5:96222400-96247200	Weak transcription	Psoas Muscle	Psoas
17	chr5:96222400-96258200	Weak transcription	Stomach Mucosa	stomach
18	chr5:96223200-96240400	Strong transcription	Liver	Liver
19	chr5:96223600-96240600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr5:96225200-96244600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:96225600-96245200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:96225600-96266400	Weak transcription	Gastric	stomach
23	chr5:96226200-96244000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:96226400-96237000	Weak transcription	Placenta	Placenta
25	chr5:96229200-96245400	Weak transcription	HSMMtube	muscle
26	chr5:96229600-96237000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:96229600-96238600	Weak transcription	HSMM	muscle
28	chr5:96229600-96238800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:96229600-96239000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:96229600-96245000	Weak transcription	NH-A	brain
31	chr5:96229600-96269600	Weak transcription	Aorta	Aorta
32	chr5:96229800-96237200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:96229800-96241600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:96229800-96256800	Weak transcription	NHEK	skin
35	chr5:96229800-96256800	Weak transcription	Osteobl	bone
36	chr5:96229800-96257000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:96229800-96270000	Weak transcription	Esophagus	oesophagus
38	chr5:96230200-96237800	Weak transcription	Colonic Mucosa	Colon
39	chr5:96231000-96239800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:96231800-96245000	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:96232600-96237000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:96232600-96240400	Strong transcription	Adipose Nuclei	Adipose
43	chr5:96232600-96240800	Weak transcription	Fetal Heart	heart
44	chr5:96232600-96258400	Weak transcription	Brain Hippocampus Middle	brain
45	chr5:96232800-96242000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr5:96233000-96255600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:96233000-96256200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr5:96233200-96239000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:96233200-96240200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr5:96233200-96240600	Strong transcription	Primary T cells from cord blood	blood

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