Variant report

Variant	rs2549780
Chromosome Location	chr5:96216784-96216785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000164308	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1230360	0.90[ASN][1000 genomes]
rs1230361	0.94[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs1230363	0.87[ASN][1000 genomes]
rs1230364	0.89[ASN][1000 genomes]
rs1230365	0.87[ASN][1000 genomes]
rs1235617	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs2549779	0.94[ASW][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2617436	0.94[ASW][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs968218	0.84[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2549780	ERAP2	cis	Esophagus Muscularis	GTEx
rs2549780	ERAP2	cis	Muscle Skeletal	GTEx
rs2549780	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs2549780	LRAP	cis	uninvolved skin	skin_eQTL
rs2549780	ERAP2	cis	Whole Blood	GTEx
rs2549780	LNPEP	cis	brain	seeQTL
rs2549780	ERAP2	cis	parietal	SCAN
rs2549780	LRAP	cis	multi-tissue	Pritchard
rs2549780	ERAP2	cis	cerebellum	SCAN
rs2549780	ERAP2	cis	Esophagus Mucosa	GTEx
rs2549780	ERAP2	cis	Adipose Subcutaneous	GTEx
rs2549780	LRAP	cis	lesional skin	skin_eQTL
rs2549780	LRAP	cis	normal skin	skin_eQTL
rs2549780	ERAP2	cis	lymphoblastoid	seeQTL
rs2549780	ERAP1	cis	cerebellum	SCAN
rs2549780	ERAP2	cis	Artery Tibial	GTEx
rs2549780	ERAP2	cis	lung	GTEx

Chromatin state (count:98 , 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	chr5:96213000-96217000	Weak transcription	Lung	lung
10	chr5:96213000-96217200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:96213000-96239000	Weak transcription	Pancreas	Pancrea
12	chr5:96213200-96217000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:96213200-96217000	Weak transcription	Psoas Muscle	Psoas
14	chr5:96213200-96217200	Weak transcription	HSMM	muscle
15	chr5:96213200-96217400	Weak transcription	Right Ventricle	heart
16	chr5:96213200-96221600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:96213200-96225200	Weak transcription	Ovary	ovary
18	chr5:96213200-96229200	Weak transcription	Aorta	Aorta
19	chr5:96213400-96216800	Weak transcription	Colonic Mucosa	Colon
20	chr5:96213400-96216800	Weak transcription	Fetal Intestine Small	intestine
21	chr5:96213400-96217000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:96213400-96217000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:96213400-96217000	Weak transcription	Right Atrium	heart
24	chr5:96213400-96217200	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:96213400-96217200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:96213400-96217600	Weak transcription	Brain Anterior Caudate	brain
27	chr5:96213400-96219000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:96213400-96221400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:96213400-96221600	Weak transcription	Brain Angular Gyrus	brain
30	chr5:96213400-96223600	Weak transcription	Fetal Kidney	kidney
31	chr5:96213400-96237800	Weak transcription	Brain Substantia Nigra	brain
32	chr5:96213400-96243800	Weak transcription	HepG2	liver
33	chr5:96213400-96247000	Weak transcription	Fetal Lung	lung
34	chr5:96213600-96216800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:96213600-96216800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:96213600-96217400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:96213800-96217000	Weak transcription	Liver	Liver
38	chr5:96213800-96217600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:96214400-96216800	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr5:96214400-96217000	Weak transcription	Fetal Intestine Large	intestine
41	chr5:96214600-96221400	Weak transcription	Esophagus	oesophagus
42	chr5:96215200-96217000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr5:96215200-96218200	Enhancers	Stomach Mucosa	stomach
44	chr5:96215200-96218600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
45	chr5:96215200-96221200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:96215400-96216800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr5:96215400-96217600	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr5:96215400-96217600	Genic enhancers	Primary hematopoietic stem cells	blood
49	chr5:96215400-96217600	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr5:96215400-96217600	Strong transcription	Fetal Muscle Trunk	muscle

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