Variant report

Variant	rs3733904
Chromosome Location	chr5:96216173-96216174
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	SPI1	chr5:96216122-96216522	HL-60	blood:	n/a	chr5:96216336-96216349 chr5:96216342-96216351 chr5:96216339-96216346 chr5:96216335-96216348
2	IKZF1	chr5:96216099-96216572	GM12878	blood:	n/a	n/a
3	RELA	chr5:96215350-96216301	GM12891	blood:	n/a	n/a
4	POLR2A	chr5:96215646-96216578	HUVEC	blood vessel:	n/a	n/a
5	SPI1	chr5:96216082-96216473	GM12891	blood:	n/a	chr5:96216336-96216349 chr5:96216342-96216351 chr5:96216339-96216346 chr5:96216335-96216348
6	GATA2	chr5:96216012-96216481	HUVEC	blood vessel:	n/a	chr5:96216279-96216289 chr5:96216339-96216349 chr5:96216090-96216100
7	FOS	chr5:96216094-96216565	MCF10A-Er-Src	breast:	n/a	chr5:96216280-96216289 chr5:96216141-96216152 chr5:96216378-96216386 chr5:96216378-96216385 chr5:96216378-96216387 chr5:96216376-96216387
8	POLR2A	chr5:96216069-96216431	HUVEC	blood vessel:	n/a	n/a
9	FOS	chr5:96216113-96216561	MCF10A-Er-Src	breast:	n/a	chr5:96216280-96216289 chr5:96216141-96216152 chr5:96216378-96216386 chr5:96216378-96216385 chr5:96216378-96216387 chr5:96216376-96216387
10	POLR2A	chr5:96215869-96216788	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr5:96215954-96216523	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr5:96216012-96216475	U87	brain:	n/a	n/a
13	POLR2A	chr5:96216012-96216502	U87	brain:	n/a	n/a
14	FOSL1	chr5:96216135-96216537	HCT-116	colon:	n/a	chr5:96216280-96216289 chr5:96216141-96216152 chr5:96216378-96216386 chr5:96216378-96216385 chr5:96216378-96216387
15	JUN	chr5:96216075-96216551	HUVEC	blood vessel:	n/a	chr5:96216280-96216289 chr5:96216141-96216152 chr5:96216378-96216386 chr5:96216378-96216385 chr5:96216378-96216387
16	FOS	chr5:96216001-96216720	HUVEC	blood vessel:	n/a	chr5:96216002-96216011 chr5:96216280-96216289 chr5:96216141-96216152 chr5:96216378-96216386 chr5:96216378-96216385 chr5:96216378-96216387 chr5:96216376-96216387
17	SPI1	chr5:96216121-96216504	GM12891	blood:	n/a	chr5:96216336-96216349 chr5:96216342-96216351 chr5:96216339-96216346 chr5:96216335-96216348
18	POLR2A	chr5:96215876-96216588	U87	brain:	n/a	n/a
19	FOS	chr5:96216157-96216571	MCF10A-Er-Src	breast:	n/a	chr5:96216280-96216289 chr5:96216378-96216386 chr5:96216378-96216385 chr5:96216378-96216387 chr5:96216376-96216387
20	POLR2A	chr5:96215791-96216799	HUVEC	blood vessel:	n/a	n/a
21	FOSL2	chr5:96215994-96216660	SK-N-SH	brain:	n/a	chr5:96216002-96216011 chr5:96216280-96216289 chr5:96216141-96216152 chr5:96216378-96216386 chr5:96216378-96216385 chr5:96216378-96216387

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96211294..96213902-chr5:96214706..96216915,2	MCF-7	breast:
2	chr5:96210113..96212141-chr5:96215069..96217476,2	K562	blood:

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

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11135481	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1134681	0.83[ASN][1000 genomes]
rs11746397	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17087180	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17515806	0.83[ASN][1000 genomes]
rs17550822	0.83[ASN][1000 genomes]
rs27731	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3733905	0.87[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3797787	1.00[JPT][hapmap]
rs3797792	1.00[JPT][hapmap]
rs3806936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806939	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3806941	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3806942	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3806943	0.83[ASN][1000 genomes]
rs3806944	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3822679	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3822687	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4397149	0.83[ASN][1000 genomes]
rs4509047	0.81[ASN][1000 genomes]
rs62376451	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62376452	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6862437	0.83[ASN][1000 genomes]
rs6883674	0.83[ASN][1000 genomes]
rs6883859	0.83[ASN][1000 genomes]
rs7714122	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7721014	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7728999	0.83[ASN][1000 genomes]
rs7729489	0.83[ASN][1000 genomes]
rs7733301	1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3733904	LRAP	cis	multi-tissue	Pritchard
rs3733904	ERAP2	cis	Esophagus Muscularis	GTEx
rs3733904	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs3733904	ERAP2	cis	intralobular white matter	BrainEAC
rs3733904	ERAP2	cis	brain	BrainEAC
rs3733904	ERAP2	cis	Whole Blood	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96211800-96217400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:96212200-96217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:96212200-96217000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:96212600-96217000	Weak transcription	Gastric	stomach
5	chr5:96212600-96217200	Weak transcription	Fetal Heart	heart
6	chr5:96212600-96232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:96212800-96217200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:96212800-96220000	Weak transcription	Fetal Stomach	stomach
9	chr5:96213000-96216400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:96213000-96217000	Weak transcription	Lung	lung
11	chr5:96213000-96217200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:96213000-96239000	Weak transcription	Pancreas	Pancrea
13	chr5:96213200-96217000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:96213200-96217000	Weak transcription	Psoas Muscle	Psoas
15	chr5:96213200-96217200	Weak transcription	HSMM	muscle
16	chr5:96213200-96217400	Weak transcription	Right Ventricle	heart
17	chr5:96213200-96221600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:96213200-96225200	Weak transcription	Ovary	ovary
19	chr5:96213200-96229200	Weak transcription	Aorta	Aorta
20	chr5:96213400-96216200	Weak transcription	K562	blood
21	chr5:96213400-96216200	Weak transcription	Osteobl	bone
22	chr5:96213400-96216800	Weak transcription	Colonic Mucosa	Colon
23	chr5:96213400-96216800	Weak transcription	Fetal Intestine Small	intestine
24	chr5:96213400-96217000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:96213400-96217000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:96213400-96217000	Weak transcription	Right Atrium	heart
27	chr5:96213400-96217200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:96213400-96217200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:96213400-96217600	Weak transcription	Brain Anterior Caudate	brain
30	chr5:96213400-96219000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:96213400-96221400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:96213400-96221600	Weak transcription	Brain Angular Gyrus	brain
33	chr5:96213400-96223600	Weak transcription	Fetal Kidney	kidney
34	chr5:96213400-96237800	Weak transcription	Brain Substantia Nigra	brain
35	chr5:96213400-96243800	Weak transcription	HepG2	liver
36	chr5:96213400-96247000	Weak transcription	Fetal Lung	lung
37	chr5:96213600-96216800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:96213600-96216800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:96213600-96217400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:96213800-96216400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:96213800-96216600	Weak transcription	Adipose Nuclei	Adipose
42	chr5:96213800-96217000	Weak transcription	Liver	Liver
43	chr5:96213800-96217600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:96214400-96216200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:96214400-96216800	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr5:96214400-96217000	Weak transcription	Fetal Intestine Large	intestine
47	chr5:96214600-96221400	Weak transcription	Esophagus	oesophagus
48	chr5:96215200-96216200	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr5:96215200-96217000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr5:96215200-96218200	Enhancers	Stomach Mucosa	stomach

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