Variant report

Variant	rs27043
Chromosome Location	chr5:96117300-96117301
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	MAFK	chr5:96117199-96117629	HepG2	liver:	n/a	chr5:96117263-96117278
2	FOXA1	chr5:96117210-96117773	HepG2	liver:	n/a	n/a
3	FOXA1	chr5:96117291-96117790	HepG2	liver:	n/a	n/a
4	CEBPB	chr5:96116716-96117308	Hela-S3	cervix:	n/a	n/a
5	NFIC	chr5:96116416-96117533	SK-N-SH	brain:	n/a	n/a
6	MAFK	chr5:96117247-96117305	HepG2	liver:	n/a	chr5:96117263-96117278
7	TCF7L2	chr5:96116415-96117570	PANC-1	pancreas:	n/a	n/a
8	FOSL1	chr5:96116584-96117354	HCT-116	colon:	n/a	n/a
9	MAFF	chr5:96117239-96117439	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:96116271-96119823	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr5:96116643-96117337	HCT-116	colon:	n/a	n/a
12	POLR2A	chr5:96113372-96117735	K562	blood:	n/a	n/a
13	STAT3	chr5:96116777-96117374	MCF10A-Er-Src	breast:	n/a	n/a
14	EP300	chr5:96117195-96117557	SK-N-SH_RA	brain:	n/a	n/a
15	STAT3	chr5:96116669-96117463	MCF10A-Er-Src	breast:	n/a	n/a
16	SIN3AK20	chr5:96117175-96117605	PFSK-1	brain:	n/a	n/a
17	FOS	chr5:96116667-96117383	MCF10A-Er-Src	breast:	n/a	chr5:96116953-96116964
18	STAT3	chr5:96116800-96117339	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:96117181-96117525	HepG2	liver:	n/a	n/a
20	JUND	chr5:96116525-96117324	HCT-116	colon:	n/a	n/a
21	REST	chr5:96117178-96117558	PFSK-1	brain:	n/a	n/a
22	GATA2	chr5:96116352-96117511	HUVEC	blood vessel:	n/a	chr5:96116425-96116435
23	GATA3	chr5:96116341-96117376	SK-N-SH	brain:	n/a	chr5:96116425-96116435
24	FOS	chr5:96116665-96117372	MCF10A-Er-Src	breast:	n/a	chr5:96116953-96116964
25	FOXA2	chr5:96117228-96117819	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:96116061-96117912	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr5:96117286-96117708	PANC-1	pancreas:	n/a	n/a
28	REST	chr5:96117227-96117699	PFSK-1	brain:	n/a	n/a
29	GATA3	chr5:96116295-96117643	SK-N-SH	brain:	n/a	chr5:96116425-96116435
30	POLR2A	chr5:96117048-96118023	PFSK-1	brain:	n/a	n/a
31	TAF1	chr5:96117185-96117781	PFSK-1	brain:	n/a	n/a
32	SIN3AK20	chr5:96117168-96117612	PFSK-1	brain:	n/a	n/a
33	STAT3	chr5:96116728-96117447	MCF10A-Er-Src	breast:	n/a	n/a
34	FOXA1	chr5:96117287-96117743	HepG2	liver:	n/a	n/a
35	STAT3	chr5:96116835-96117418	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96115268..96118088-chr5:96119374..96122248,2	K562	blood:
2	chr5:96076844..96078562-chr5:96116858..96119670,2	K562	blood:

Variant related genes	Relation type
ENSG00000248734	TF binding region
ERAP1	TF binding region
ENSG00000153113	Chromatin interaction
ENSG00000248734	Chromatin interaction
ENSG00000249180	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12054720	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs1230366	0.84[ASN][1000 genomes]
rs12519842	0.84[ASN][1000 genomes]
rs12659825	0.84[ASN][1000 genomes]
rs149189	0.82[ASN][1000 genomes]
rs151823	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[ASN][1000 genomes]
rs151940	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs151964	0.83[ASN][1000 genomes]
rs152468	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs184971	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2042381	0.86[ASN][1000 genomes]
rs2351012	0.84[ASN][1000 genomes]
rs2351013	0.84[ASN][1000 genomes]
rs245472	0.86[ASN][1000 genomes]
rs246453	0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs246454	0.86[ASN][1000 genomes]
rs246455	0.86[ASN][1000 genomes]
rs249960	0.86[ASN][1000 genomes]
rs2545629	0.86[ASN][1000 genomes]
rs2549804	0.84[ASN][1000 genomes]
rs2549805	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs26489	0.83[ASN][1000 genomes]
rs26491	0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs26492	0.88[GIH][hapmap]
rs26493	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26495	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs26496	0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs26497	0.82[ASN][1000 genomes]
rs26498	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs26499	0.80[JPT][hapmap]
rs26500	0.83[ASN][1000 genomes]
rs26510	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs26512	0.82[ASN][1000 genomes]
rs26654	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs27038	0.84[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs27041	0.84[CEU][hapmap];0.94[EUR][1000 genomes]
rs27044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs27045	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs27432	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs27433	0.81[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs27434	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs27529	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs27619	0.83[JPT][hapmap]
rs27640	0.83[ASN][1000 genomes]
rs27694	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs27710	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs28081	0.88[GIH][hapmap]
rs28119	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs28333	0.83[ASN][1000 genomes]
rs28337	0.83[ASN][1000 genomes]
rs2911138	0.82[ASN][1000 genomes]
rs2911139	0.86[ASN][1000 genomes]
rs2927619	0.84[ASN][1000 genomes]
rs2927620	0.84[ASN][1000 genomes]
rs30185	0.83[ASN][1000 genomes]
rs30186	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs30187	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs30376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs30378	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs30379	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs30380	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs34735	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs39840	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39841	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3985002	0.84[ASN][1000 genomes]
rs42398	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467735	0.86[ASN][1000 genomes]
rs469674	0.81[ASN][1000 genomes]
rs469758	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs469783	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs61112531	0.84[ASN][1000 genomes]
rs709668	0.85[ASN][1000 genomes]
rs845028	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs27043	LRAP	cis	multi-tissue	Pritchard
rs27043	ERAP2	cis	lymphoblastoid	seeQTL
rs27043	ERAP1	cis	Esophagus Mucosa	GTEx
rs27043	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs27043	C5orf36	cis	parietal	SCAN
rs27043	FAM174A	cis	cerebellum	SCAN
rs27043	ERAP1	cis	lung	GTEx
rs27043	ERAP1	cis	multi-tissue	Pritchard
rs27043	CHD1	cis	cerebellum	SCAN
rs27043	ERAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs27043	ERAP2	cis	cerebellum	SCAN
rs27043	CAST	cis	parietal	SCAN
rs27043	CAST	cis	cerebellum	SCAN
rs27043	ERAP1	cis	Whole Blood	GTEx
rs27043	ERAP2	cis	parietal	SCAN
rs27043	ARTS-1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr5:96068600-96130000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:96071400-96126600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:96075200-96120400	Weak transcription	Fetal Brain Female	brain
6	chr5:96079400-96126600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:96079600-96123600	Strong transcription	Placenta	Placenta
8	chr5:96079600-96126400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:96079600-96126600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:96079600-96126600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:96092800-96126600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:96096400-96122800	Strong transcription	Primary B cells from cord blood	blood
14	chr5:96097400-96118000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:96097400-96130000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr5:96097400-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr5:96097600-96119200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr5:96097800-96126600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:96097800-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:96098000-96129600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
23	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
24	chr5:96098200-96122600	Strong transcription	Primary T cells from cord blood	blood
25	chr5:96098200-96128000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr5:96098400-96118600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:96100200-96127000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:96101200-96119600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:96104200-96136400	Strong transcription	Dnd41	blood
30	chr5:96104800-96126600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:96105000-96124400	Weak transcription	Aorta	Aorta
32	chr5:96105000-96127800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:96107600-96129600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:96107800-96138200	Strong transcription	GM12878-XiMat	blood
35	chr5:96108000-96129600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:96109600-96119800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:96110200-96130200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr5:96110400-96121800	Strong transcription	Thymus	Thymus
39	chr5:96110400-96122800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:96110400-96125600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:96110600-96117800	Strong transcription	Psoas Muscle	Psoas
42	chr5:96110600-96130400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:96111600-96126800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:96112800-96123800	Weak transcription	Brain Angular Gyrus	brain
45	chr5:96113200-96119000	Strong transcription	K562	blood
46	chr5:96113800-96117600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:96113800-96137200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:96114000-96119600	Weak transcription	Brain Anterior Caudate	brain
49	chr5:96114000-96126400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:96114400-96122600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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