Variant report

Variant	rs2549798
Chromosome Location	chr5:96245903-96245904
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96244061..96247002-chr5:96270287..96272156,2	MCF-7	breast:
2	chr5:96244332..96247286-chr5:96269247..96272076,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247121	Chromatin interaction
ENSG00000113441	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10061936	0.85[EUR][1000 genomes]
rs10069361	0.88[EUR][1000 genomes]
rs10071975	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10076136	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1019503	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10463196	0.83[ASN][1000 genomes]
rs1046396	0.81[AFR][1000 genomes]
rs1056893	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11135485	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1216565	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1216568	0.85[EUR][1000 genomes]
rs1216569	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1216570	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1230381	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230382	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12516666	0.84[ASN][1000 genomes]
rs12716486	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13163165	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1363975	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1363977	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423566	0.81[AFR][1000 genomes]
rs1423568	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1559267	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17087165	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs171647	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1820149	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs187265	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193993	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs193994	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1981846	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2042383	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2042385	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2112974	0.86[EUR][1000 genomes]
rs2113050	0.86[EUR][1000 genomes]
rs2113189	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2113190	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2113191	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2161657	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2161658	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247650	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2248374	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255546	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255633	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255634	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255637	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287988	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432141	0.81[AFR][1000 genomes]
rs251339	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs251342	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs251344	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548520	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2548521	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548522	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2548523	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548524	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548526	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548527	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548528	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548529	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548533	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548534	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548535	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548536	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548537	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548538	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548539	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548540	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549781	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549782	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549784	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549785	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549786	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2549787	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549788	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549789	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549790	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549791	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549792	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549795	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549796	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549797	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2549799	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549800	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2549801	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2617434	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs27292	0.83[EUR][1000 genomes]
rs27294	0.81[EUR][1000 genomes]
rs27305	0.83[EUR][1000 genomes]
rs27397	0.83[EUR][1000 genomes]
rs27613	0.81[EUR][1000 genomes]
rs2762	0.81[AFR][1000 genomes]
rs27747	0.83[EUR][1000 genomes]
rs2910686	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2910688	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2910787	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2910789	0.81[AFR][1000 genomes]
rs2927608	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3096167	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs31398	0.81[EUR][1000 genomes]
rs33934033	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734015	0.84[ASN][1000 genomes]
rs38030	0.81[EUR][1000 genomes]
rs38035	0.87[EUR][1000 genomes]
rs38036	0.87[EUR][1000 genomes]
rs38037	0.84[EUR][1000 genomes]
rs38040	0.81[EUR][1000 genomes]
rs38041	0.83[EUR][1000 genomes]
rs38042	0.83[EUR][1000 genomes]
rs3849750	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42983	0.81[EUR][1000 genomes]
rs4869314	0.85[ASN][1000 genomes]
rs56197090	0.84[ASN][1000 genomes]
rs6556943	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6859160	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6870825	0.88[EUR][1000 genomes]
rs6873441	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6874656	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6879678	0.84[EUR][1000 genomes]
rs7700332	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7713127	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7722694	0.86[EUR][1000 genomes]
rs7736466	0.92[EUR][1000 genomes];0.88[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
rs2549798	ERAP2	cis	Esophagus Mucosa	GTEx
rs2549798	ERAP2	cis	lung	GTEx
rs2549798	ERAP2	cis	Esophagus Muscularis	GTEx
rs2549798	ERAP2	cis	Adipose Subcutaneous	GTEx
rs2549798	ERAP2	cis	Nerve Tibial	GTEx
rs2549798	ERAP2	cis	Whole Blood	GTEx
rs2549798	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs2549798	ERAP2	cis	Heart Left Ventricle	GTEx
rs2549798	ERAP2	cis	Thyroid	GTEx
rs2549798	ERAP2	cis	Artery Aorta	GTEx
rs2549798	ERAP2	cis	Artery Tibial	GTEx
rs2549798	ERAP2	cis	Muscle Skeletal	GTEx
rs2549798	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs2549798	ERAP2	cis	Stomach	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96213400-96247000	Weak transcription	Fetal Lung	lung
2	chr5:96217600-96250000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:96218000-96264600	Weak transcription	Right Ventricle	heart
4	chr5:96218600-96259600	Weak transcription	HMEC	breast
5	chr5:96221600-96269200	Weak transcription	Fetal Brain Male	brain
6	chr5:96222000-96268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:96222400-96247200	Weak transcription	Psoas Muscle	Psoas
8	chr5:96222400-96258200	Weak transcription	Stomach Mucosa	stomach
9	chr5:96225600-96266400	Weak transcription	Gastric	stomach
10	chr5:96229600-96269600	Weak transcription	Aorta	Aorta
11	chr5:96229800-96256800	Weak transcription	NHEK	skin
12	chr5:96229800-96256800	Weak transcription	Osteobl	bone
13	chr5:96229800-96257000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:96229800-96270000	Weak transcription	Esophagus	oesophagus
15	chr5:96232600-96258400	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:96233000-96255600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:96233000-96256200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr5:96233600-96246000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:96233600-96247600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:96233800-96256000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr5:96234200-96255600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:96237400-96269200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:96237600-96250600	Weak transcription	Hela-S3	cervix
24	chr5:96237800-96265000	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:96238400-96256800	Weak transcription	NHDF-Ad	bronchial
26	chr5:96239400-96256800	Weak transcription	HSMM	muscle
27	chr5:96239400-96257200	Weak transcription	NHLF	lung
28	chr5:96239600-96252800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:96239800-96268000	Weak transcription	Colonic Mucosa	Colon
30	chr5:96240200-96253600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:96240400-96254200	Strong transcription	GM12878-XiMat	blood
32	chr5:96240600-96256800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:96242000-96259800	Weak transcription	Fetal Stomach	stomach
34	chr5:96242200-96255600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:96242200-96256000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr5:96242200-96268000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:96243200-96246000	Strong transcription	Primary T cells from cord blood	blood
38	chr5:96243200-96246000	Strong transcription	Adipose Nuclei	Adipose
39	chr5:96243200-96246600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr5:96243400-96257200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:96243600-96247200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:96243600-96255000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:96243600-96266400	Weak transcription	Brain Angular Gyrus	brain
44	chr5:96243800-96246000	Strong transcription	Fetal Intestine Large	intestine
45	chr5:96243800-96246200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:96243800-96246200	Enhancers	HepG2	liver
47	chr5:96243800-96247000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr5:96243800-96247400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:96243800-96247600	Strong transcription	Dnd41	blood
50	chr5:96243800-96256000	Strong transcription	Fetal Thymus	thymus

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