Variant report

Variant	rs12189125
Chromosome Location	chr5:96221011-96221012
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	NFIC	chr5:96220784-96222305	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:96220746-96221089	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96219913..96223749-chr5:96224783..96226806,3	MCF-7	breast:
2	chr5:96215750..96217350-chr5:96220796..96223621,2	K562	blood:
3	chr5:96219096..96221374-chr5:96270247..96273227,3	MCF-7	breast:
4	chr5:96211554..96214084-chr5:96217636..96221209,3	K562	blood:

Variant related genes	Relation type
ERAP2	TF binding region
ENSG00000113441	Chromatin interaction
ENSG00000247121	Chromatin interaction
ENSG00000164308	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1019503	0.83[ASN][1000 genomes]
rs10434708	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434709	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056893	0.86[ASN][1000 genomes]
rs11135483	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11135484	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11135485	0.81[ASN][1000 genomes]
rs11750025	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216565	0.84[ASN][1000 genomes]
rs1216569	0.84[ASN][1000 genomes]
rs1216570	0.83[ASN][1000 genomes]
rs1230381	0.83[ASN][1000 genomes]
rs1230382	0.83[ASN][1000 genomes]
rs12516666	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12653964	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12654015	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655858	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13167902	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13189819	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363975	0.83[ASN][1000 genomes]
rs1363977	0.83[ASN][1000 genomes]
rs1423568	0.86[ASN][1000 genomes]
rs1559354	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559355	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559357	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17087165	0.86[ASN][1000 genomes]
rs171647	0.86[ASN][1000 genomes]
rs187265	0.86[ASN][1000 genomes]
rs193993	0.87[ASN][1000 genomes]
rs1981846	0.84[ASN][1000 genomes]
rs2042383	0.87[ASN][1000 genomes]
rs2042385	0.83[ASN][1000 genomes]
rs2113189	0.87[ASN][1000 genomes]
rs2113190	0.86[ASN][1000 genomes]
rs2113191	0.86[ASN][1000 genomes]
rs2161657	0.86[ASN][1000 genomes]
rs2161658	0.86[ASN][1000 genomes]
rs2247650	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2248374	0.86[ASN][1000 genomes]
rs2255546	0.83[ASN][1000 genomes]
rs2255633	0.83[ASN][1000 genomes]
rs2255634	0.83[ASN][1000 genomes]
rs2255637	0.83[ASN][1000 genomes]
rs2278018	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278019	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287988	0.86[ASN][1000 genomes]
rs251342	0.86[ASN][1000 genomes]
rs251344	0.81[ASN][1000 genomes]
rs2548521	0.81[ASN][1000 genomes]
rs2548522	0.83[ASN][1000 genomes]
rs2548523	0.86[ASN][1000 genomes]
rs2548524	0.86[ASN][1000 genomes]
rs2548526	0.86[ASN][1000 genomes]
rs2548527	0.86[ASN][1000 genomes]
rs2548528	0.86[ASN][1000 genomes]
rs2548529	0.86[ASN][1000 genomes]
rs2548533	0.86[ASN][1000 genomes]
rs2548534	0.87[ASN][1000 genomes]
rs2548535	0.87[ASN][1000 genomes]
rs2548536	0.87[ASN][1000 genomes]
rs2548537	0.87[ASN][1000 genomes]
rs2548538	0.87[ASN][1000 genomes]
rs2548539	0.87[ASN][1000 genomes]
rs2548540	0.87[ASN][1000 genomes]
rs2549781	0.87[ASN][1000 genomes]
rs2549782	0.87[ASN][1000 genomes]
rs2549784	0.87[ASN][1000 genomes]
rs2549785	0.87[ASN][1000 genomes]
rs2549787	0.86[ASN][1000 genomes]
rs2549788	0.86[ASN][1000 genomes]
rs2549789	0.86[ASN][1000 genomes]
rs2549790	0.86[ASN][1000 genomes]
rs2549791	0.86[ASN][1000 genomes]
rs2549792	0.84[ASN][1000 genomes]
rs2549795	0.86[ASN][1000 genomes]
rs2549796	0.86[ASN][1000 genomes]
rs2549797	0.86[ASN][1000 genomes]
rs2549800	0.82[ASN][1000 genomes]
rs2549801	0.83[ASN][1000 genomes]
rs2910686	0.82[ASN][1000 genomes]
rs2910688	0.81[ASN][1000 genomes]
rs33934033	0.86[ASN][1000 genomes]
rs3734015	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3849750	0.87[ASN][1000 genomes]
rs4869311	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869312	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869313	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4869314	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55770741	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56197090	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6556942	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6556943	0.87[ASN][1000 genomes]
rs6859160	0.86[ASN][1000 genomes]
rs6868302	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873441	0.86[ASN][1000 genomes]
rs6874656	0.87[ASN][1000 genomes]
rs7713127	0.81[ASN][1000 genomes]
rs7721944	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736466	0.81[ASN][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12189125	ERAP2	cis	Nerve Tibial	GTEx
rs12189125	ERAP2	cis	Esophagus Mucosa	GTEx
rs12189125	ERAP2	cis	Heart Left Ventricle	GTEx
rs12189125	ERAP2	cis	Artery Aorta	GTEx
rs12189125	ERAP2	cis	Whole Blood	GTEx
rs12189125	ERAP2	cis	Adipose Subcutaneous	GTEx
rs12189125	ERAP2	cis	Thyroid	GTEx
rs12189125	ERAP2	cis	Stomach	GTEx
rs12189125	ERAP2	cis	Esophagus Muscularis	GTEx
rs12189125	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs12189125	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs12189125	ERAP2	cis	Muscle Skeletal	GTEx
rs12189125	AC008865.1	cis	Artery Tibial	GTEx
rs12189125	ERAP2	cis	Artery Tibial	GTEx
rs12189125	ERAP2	cis	lung	GTEx

Chromatin state (count:98 , 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	chr5:96213200-96221600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:96213200-96225200	Weak transcription	Ovary	ovary
5	chr5:96213200-96229200	Weak transcription	Aorta	Aorta
6	chr5:96213400-96221400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:96213400-96221600	Weak transcription	Brain Angular Gyrus	brain
8	chr5:96213400-96223600	Weak transcription	Fetal Kidney	kidney
9	chr5:96213400-96237800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:96213400-96243800	Weak transcription	HepG2	liver
11	chr5:96213400-96247000	Weak transcription	Fetal Lung	lung
12	chr5:96214600-96221400	Weak transcription	Esophagus	oesophagus
13	chr5:96215200-96221200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:96215400-96222400	Genic enhancers	Fetal Thymus	thymus
15	chr5:96217000-96221200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:96217200-96222600	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr5:96217400-96221800	Genic enhancers	Dnd41	blood
18	chr5:96217400-96229200	Weak transcription	Colonic Mucosa	Colon
19	chr5:96217600-96221200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr5:96217600-96228800	Weak transcription	HSMM	muscle
21	chr5:96217600-96241600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:96217600-96250000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:96217800-96221400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:96217800-96224600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:96217800-96225200	Weak transcription	Gastric	stomach
26	chr5:96217800-96228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:96217800-96229200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:96217800-96229200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:96217800-96237800	Weak transcription	NHDF-Ad	bronchial
30	chr5:96218000-96221200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:96218000-96221400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:96218000-96221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:96218000-96222600	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr5:96218000-96222600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr5:96218000-96222600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:96218000-96225200	Weak transcription	Spleen	Spleen
37	chr5:96218000-96229000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:96218000-96229000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:96218000-96229200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:96218000-96237000	Weak transcription	NHLF	lung
41	chr5:96218000-96264600	Weak transcription	Right Ventricle	heart
42	chr5:96218200-96221200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr5:96218200-96221200	Weak transcription	K562	blood
44	chr5:96218200-96221400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:96218200-96221400	Weak transcription	Stomach Mucosa	stomach
46	chr5:96218200-96221400	Weak transcription	Osteobl	bone
47	chr5:96218200-96222200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:96218200-96228600	Weak transcription	NH-A	brain
49	chr5:96218200-96228800	Weak transcription	NHEK	skin
50	chr5:96218200-96231400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links