Variant report

Variant	rs1230361
Chromosome Location	chr5:96213171-96213172
allele	A/C
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	GATA3	chr5:96213093-96213249	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr5:96212880-96213198	T-47D	breast:	n/a	chr5:96213076-96213092 chr5:96213076-96213092 chr5:96213073-96213094
3	GATA1	chr5:96212888-96213530	PBDE	blood:	n/a	chr5:96213076-96213092 chr5:96213076-96213092 chr5:96213483-96213495 chr5:96213073-96213094
4	MAZ	chr5:96212967-96213289	K562	blood:	n/a	n/a
5	POLR2A	chr5:96213008-96213269	MCF10A-Er-Src	breast:	n/a	n/a
6	IRF1	chr5:96211340-96213330	K562	blood:	n/a	chr5:96212173-96212190 chr5:96212168-96212182 chr5:96212170-96212184 chr5:96212176-96212190 chr5:96212166-96212186 chr5:96212174-96212184 chr5:96212171-96212185 chr5:96212179-96212196 chr5:96212168-96212189 chr5:96212174-96212185 chr5:96212172-96212192 chr5:96212172-96212185 chr5:96212172-96212185 chr5:96212174-96212188 chr5:96212172-96212185 chr5:96212175-96212186 chr5:96212169-96212180
7	GATA2	chr5:96212850-96213407	HUVEC	blood vessel:	n/a	chr5:96213076-96213092 chr5:96213076-96213092 chr5:96213073-96213094
8	IRF1	chr5:96211442-96213361	K562	blood:	n/a	chr5:96212173-96212190 chr5:96212168-96212182 chr5:96212170-96212184 chr5:96212176-96212190 chr5:96212166-96212186 chr5:96212174-96212184 chr5:96212171-96212185 chr5:96212179-96212196 chr5:96212168-96212189 chr5:96212174-96212185 chr5:96212172-96212192 chr5:96212172-96212185 chr5:96212172-96212185 chr5:96212174-96212188 chr5:96212172-96212185 chr5:96212175-96212186 chr5:96212169-96212180
9	POLR2A	chr5:96211390-96213417	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96212491..96215464-chr5:96223042..96225542,2	K562	blood:
2	chr5:96142074..96143978-chr5:96212252..96215087,2	K562	blood:
3	chr5:96210744..96214555-chr5:96268958..96271606,4	MCF-7	breast:
4	chr5:96212214..96214084-chr5:96217203..96219457,3	K562	blood:
5	chr5:96142074..96145143-chr5:96212194..96215127,3	K562	blood:
6	chr5:96207193..96215079-chr5:96269183..96273335,11	MCF-7	breast:
7	chr5:96211294..96213902-chr5:96214706..96216915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247121	TF binding region
ERAP2	TF binding region
ENSG00000164308	Chromatin interaction
ENSG00000164307	Chromatin interaction
ENSG00000247121	Chromatin interaction
ENSG00000113441	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1230360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1230364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1230365	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1235617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2549780	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]
rs2617436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4869315	0.87[MEX][hapmap]
rs968218	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs1230361	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs1230361	ERAP2	cis	Muscle Skeletal	GTEx
rs1230361	ERAP2	cis	cerebellum	SCAN
rs1230361	ERAP2	cis	Esophagus Mucosa	GTEx
rs1230361	ERAP2	cis	Adipose Subcutaneous	GTEx
rs1230361	LRAP	cis	lesional skin	skin_eQTL
rs1230361	LRAP	cis	normal skin	skin_eQTL
rs1230361	LRAP	cis	uninvolved skin	skin_eQTL
rs1230361	ERAP1	cis	cerebellum	SCAN
rs1230361	ERAP2	cis	Esophagus Muscularis	GTEx
rs1230361	ERAP2	cis	Heart Left Ventricle	GTEx
rs1230361	ERAP1	cis	lymphoblastoid	seeQTL
rs1230361	ERAP2	cis	lymphoblastoid	seeQTL
rs1230361	ERAP2	cis	parietal	SCAN
rs1230361	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs1230361	ERAP2	cis	Whole Blood	GTEx
rs1230361	ERAP2	cis	Nerve Tibial	GTEx
rs1230361	ERAP2	cis	Thyroid	GTEx
rs1230361	ERAP2	cis	Artery Tibial	GTEx
rs1230361	ERAP2	cis	lung	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96211000-96213400	Active TSS	Right Atrium	heart
2	chr5:96211400-96213200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:96211400-96213400	Active TSS	Brain Anterior Caudate	brain
4	chr5:96211400-96213800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr5:96211600-96213200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:96211600-96213200	Active TSS	Aorta	Aorta
7	chr5:96211600-96213200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr5:96211600-96213200	Active TSS	Ovary	ovary
9	chr5:96211600-96213200	Active TSS	Right Ventricle	heart
10	chr5:96211600-96213400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:96211600-96213400	Active TSS	Brain Substantia Nigra	brain
12	chr5:96211600-96213400	Active TSS	Colonic Mucosa	Colon
13	chr5:96211600-96213600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:96211800-96213200	Active TSS	Psoas Muscle	Psoas
15	chr5:96211800-96213200	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr5:96211800-96213200	Active TSS	Small Intestine	intestine
17	chr5:96211800-96213200	Active TSS	Stomach Mucosa	stomach
18	chr5:96211800-96213200	Active TSS	Hela-S3	cervix
19	chr5:96211800-96213200	Active TSS	NHDF-Ad	bronchial
20	chr5:96211800-96213400	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:96211800-96213400	Active TSS	Brain Angular Gyrus	brain
22	chr5:96211800-96213400	Active TSS	Stomach Smooth Muscle	stomach
23	chr5:96211800-96217400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:96212000-96213200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:96212000-96213200	Active TSS	HSMMtube	muscle
26	chr5:96212000-96213200	Active TSS	NHEK	skin
27	chr5:96212000-96213400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr5:96212000-96213400	Active TSS	K562	blood
29	chr5:96212000-96213600	Active TSS	Primary T cells fromperipheralblood	blood
30	chr5:96212000-96213600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:96212000-96213800	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr5:96212000-96213800	Active TSS	Thymus	Thymus
33	chr5:96212000-96214000	Active TSS	GM12878-XiMat	blood
34	chr5:96212200-96213200	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr5:96212200-96213200	Active TSS	Fetal Kidney	kidney
36	chr5:96212200-96217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:96212200-96217000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:96212600-96213800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr5:96212600-96215400	Weak transcription	Spleen	Spleen
40	chr5:96212600-96215600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:96212600-96217000	Weak transcription	Gastric	stomach
42	chr5:96212600-96217200	Weak transcription	Fetal Heart	heart
43	chr5:96212600-96232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:96212800-96213200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr5:96212800-96213200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr5:96212800-96213200	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr5:96212800-96213200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr5:96212800-96213400	Enhancers	Fetal Intestine Small	intestine
49	chr5:96212800-96213400	Enhancers	Fetal Lung	lung
50	chr5:96212800-96213600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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