Variant report

Variant	rs6887500
Chromosome Location	chr5:96277721-96277722
allele	A/G
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	POLR2A	chr5:96277605-96277837	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:96277501-96278211	GM12891	blood:	n/a	n/a
3	POLR2A	chr5:96277415-96277873	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:96277520-96277989	GM12892	blood:	n/a	n/a
5	POLR2A	chr5:96277528-96278130	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96142551..96144780-chr5:96277248..96279292,2	MCF-7	breast:
2	chr5:96275975..96278496-chr5:96297734..96299587,2	K562	blood:

Variant related genes	Relation type
ENSG00000227836	TF binding region
ENSG00000164307	Chromatin interaction
ENSG00000200884	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10038651	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10044354	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10051637	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10058476	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10061936	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10069361	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077945	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046395	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1046396	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10476696	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1056893	0.81[AFR][1000 genomes]
rs1216565	0.90[AFR][1000 genomes]
rs1216566	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1216567	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1216568	0.93[ASN][1000 genomes]
rs1216569	0.89[AFR][1000 genomes]
rs1216570	0.87[AFR][1000 genomes]
rs1216571	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13170029	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13358339	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1363907	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1363908	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1363974	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1363975	0.86[AFR][1000 genomes]
rs1363976	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1363977	0.86[AFR][1000 genomes]
rs1423357	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1423566	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477364	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1544777	0.88[EUR][1000 genomes]
rs17087165	0.81[AFR][1000 genomes]
rs18059	0.81[ASN][1000 genomes]
rs1820148	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs193994	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113191	0.81[AFR][1000 genomes]
rs2161548	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255546	0.86[AFR][1000 genomes]
rs2255633	0.86[AFR][1000 genomes]
rs2255634	0.86[AFR][1000 genomes]
rs2255637	0.86[AFR][1000 genomes]
rs2351010	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2351011	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2432141	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432142	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs251340	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs251341	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548224	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548226	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2548516	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548520	0.83[AFR][1000 genomes]
rs2548521	0.81[AFR][1000 genomes]
rs2548523	0.81[AFR][1000 genomes]
rs2548524	0.83[AFR][1000 genomes]
rs2548528	0.82[AFR][1000 genomes]
rs2548530	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2548532	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549783	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2549789	0.81[AFR][1000 genomes]
rs2549790	0.81[AFR][1000 genomes]
rs2549792	0.81[AFR][1000 genomes]
rs2549794	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2549795	0.81[AFR][1000 genomes]
rs2549797	0.81[AFR][1000 genomes]
rs2549800	0.85[AFR][1000 genomes]
rs2549801	0.86[AFR][1000 genomes]
rs2617434	0.86[AFR][1000 genomes]
rs2617435	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2617439	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2617447	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs27289	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27290	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27293	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27295	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27296	0.80[ASN][1000 genomes]
rs27298	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27299	0.80[ASN][1000 genomes]
rs27300	0.85[EUR][1000 genomes]
rs27306	0.86[EUR][1000 genomes]
rs27307	0.86[EUR][1000 genomes]
rs27436	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs27613	0.82[ASN][1000 genomes]
rs2762	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27621	0.80[ASN][1000 genomes]
rs27659	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27660	0.85[EUR][1000 genomes]
rs27711	0.85[EUR][1000 genomes]
rs27712	0.83[EUR][1000 genomes]
rs27993	0.85[EUR][1000 genomes]
rs27998	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2859491	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2910686	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2910687	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2910688	0.85[AFR][1000 genomes]
rs2910787	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2910788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2910789	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2910793	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2927608	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2927609	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs31398	0.80[ASN][1000 genomes]
rs33934033	0.81[AFR][1000 genomes]
rs3797796	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38029	0.85[EUR][1000 genomes]
rs38031	0.85[EUR][1000 genomes]
rs38032	0.88[EUR][1000 genomes]
rs38033	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38034	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38038	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38039	0.85[EUR][1000 genomes]
rs38040	0.85[ASN][1000 genomes]
rs38043	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38044	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3849749	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3909451	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39602	0.87[EUR][1000 genomes]
rs4360063	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859168	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6870825	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6871162	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6873866	0.84[AMR][1000 genomes]
rs716848	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7703341	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7705093	0.81[ASN][1000 genomes]
rs7713127	0.81[EUR][1000 genomes]
rs7716222	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7719705	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7726445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7731592	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733312	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7736466	0.81[EUR][1000 genomes]
rs9314181	0.93[EUR][1000 genomes];0.91[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6887500	ERAP2	cis	Artery Aorta	GTEx
rs6887500	ERAP2	cis	lung	GTEx
rs6887500	ERAP2	cis	Esophagus Mucosa	GTEx
rs6887500	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs6887500	ERAP2	cis	Artery Tibial	GTEx
rs6887500	ERAP2	cis	Adipose Subcutaneous	GTEx
rs6887500	ERAP2	cis	Whole Blood	GTEx
rs6887500	ERAP2	cis	Stomach	GTEx
rs6887500	ERAP2	cis	Heart Left Ventricle	GTEx
rs6887500	ERAP2	cis	Nerve Tibial	GTEx
rs6887500	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs6887500	ERAP2	cis	Muscle Skeletal	GTEx
rs6887500	ERAP2	cis	Thyroid	GTEx
rs6887500	AC008865.1	cis	Artery Tibial	GTEx
rs6887500	ERAP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96272600-96281400	Weak transcription	Spleen	Spleen
2	chr5:96272800-96279000	Weak transcription	Esophagus	oesophagus
3	chr5:96273000-96278000	Weak transcription	Lung	lung
4	chr5:96273000-96279000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:96273000-96285000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:96273000-96288000	Weak transcription	Fetal Stomach	stomach
7	chr5:96273000-96299200	Weak transcription	Aorta	Aorta
8	chr5:96273200-96279600	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:96273400-96278000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:96273400-96278400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr5:96273400-96281000	Weak transcription	Fetal Lung	lung
12	chr5:96273400-96292800	Weak transcription	K562	blood
13	chr5:96273600-96277800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:96273600-96280200	Weak transcription	HUVEC	blood vessel
15	chr5:96273800-96277800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:96273800-96278200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr5:96273800-96278800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:96273800-96283000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:96273800-96285000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:96273800-96287200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:96273800-96289600	Weak transcription	Fetal Kidney	kidney
22	chr5:96273800-96291200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:96274200-96280000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:96274400-96279000	Weak transcription	NHLF	lung
25	chr5:96274400-96279800	Weak transcription	Hela-S3	cervix
26	chr5:96274400-96282000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:96274400-96282000	Weak transcription	A549	lung
28	chr5:96274400-96288200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:96274600-96278000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr5:96274600-96279600	Weak transcription	Right Atrium	heart
31	chr5:96274600-96279600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:96274600-96281000	Weak transcription	Small Intestine	intestine
33	chr5:96274600-96281200	Weak transcription	Brain Anterior Caudate	brain
34	chr5:96274600-96281200	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:96274600-96286000	Weak transcription	Adipose Nuclei	Adipose
36	chr5:96274600-96287400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:96274600-96288000	Weak transcription	Colon Smooth Muscle	Colon
38	chr5:96274600-96288800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:96274600-96293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:96274600-96298400	Weak transcription	HSMM	muscle
41	chr5:96274800-96288400	Weak transcription	HepG2	liver
42	chr5:96275200-96279600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr5:96275800-96284400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:96275800-96284800	Weak transcription	Primary B cells from cord blood	blood
45	chr5:96276000-96288000	Weak transcription	Fetal Heart	heart
46	chr5:96276400-96277800	Enhancers	Pancreas	Pancrea
47	chr5:96276400-96278000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:96276400-96279800	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr5:96276400-96279800	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr5:96276600-96278400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links