Variant report

Variant	rs28081
Chromosome Location	chr5:96092990-96092991
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	chr5:96091229-96093308	K562	blood:	n/a	n/a
2	POLR2A	chr5:96092626-96093034	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:96092774-96093011	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
CAST	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs26492	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26507	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs27037	0.86[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs27038	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs27041	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs27043	0.88[GIH][hapmap]
rs27433	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs27524	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs27583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3822683	0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs42398	0.88[GIH][hapmap]
rs57889668	0.84[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	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	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
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28081	ERAP1	cis	lung	GTEx
rs28081	ERAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs28081	FAM174A	cis	cerebellum	SCAN
rs28081	ERAP2	cis	lymphoblastoid	seeQTL
rs28081	ERAP1	cis	Whole Blood	GTEx
rs28081	ERAP2	cis	parietal	SCAN
rs28081	CAST	cis	cerebellum	SCAN
rs28081	C5orf36	cis	parietal	SCAN
rs28081	CAST	cis	parietal	SCAN
rs28081	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs28081	ERAP1	cis	multi-tissue	Pritchard
rs28081	ERAP2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96057800-96098600	Weak transcription	Fetal Brain Male	brain
2	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
3	chr5:96068200-96095400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr5:96068200-96100400	Strong transcription	Liver	Liver
5	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr5:96068600-96130000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:96069400-96094000	Strong transcription	Fetal Muscle Leg	muscle
8	chr5:96069600-96094000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:96070200-96116400	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr5:96070800-96095400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr5:96071000-96112800	Strong transcription	Hela-S3	cervix
12	chr5:96071200-96094000	Strong transcription	HSMM	muscle
13	chr5:96071400-96113000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:96071400-96126600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:96071600-96103200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:96072600-96115600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:96072800-96094600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr5:96072800-96095200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:96072800-96095200	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr5:96073400-96115600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:96075200-96120400	Weak transcription	Fetal Brain Female	brain
22	chr5:96075800-96094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:96076000-96093400	Strong transcription	Primary T cells from cord blood	blood
24	chr5:96078000-96111200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:96078600-96095000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:96079400-96093400	Strong transcription	NHEK	skin
27	chr5:96079400-96094000	Strong transcription	Lung	lung
28	chr5:96079400-96094200	Strong transcription	Osteobl	bone
29	chr5:96079400-96094800	Strong transcription	Primary B cells from cord blood	blood
30	chr5:96079400-96096000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:96079400-96115600	Strong transcription	HMEC	breast
32	chr5:96079400-96126600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr5:96079600-96093600	Strong transcription	NH-A	brain
34	chr5:96079600-96094800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:96079600-96112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:96079600-96115400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:96079600-96115600	Strong transcription	NHDF-Ad	bronchial
38	chr5:96079600-96123600	Strong transcription	Placenta	Placenta
39	chr5:96079600-96126400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:96079600-96126600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr5:96079600-96126600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr5:96079800-96094600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:96079800-96095200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:96082000-96095800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:96082400-96098400	Weak transcription	Dnd41	blood
46	chr5:96083400-96094800	Strong transcription	Colon Smooth Muscle	Colon
47	chr5:96083800-96096000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:96083800-96108800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr5:96083800-96116400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr5:96084200-96093600	Strong transcription	Spleen	Spleen

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