Variant report

Variant	rs42398
Chromosome Location	chr5:96120455-96120456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:96120272-96120508	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:96120273-96120830	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:96119663-96122731	A549	lung:	n/a	n/a
4	POLR2A	chr5:96120084-96120920	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr5:96120165-96120544	U87	brain:	n/a	n/a
6	POLR2A	chr5:96118093-96122778	K562	blood:	n/a	n/a
7	POLR2A	chr5:96120334-96120511	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:96120043-96120910	U87	brain:	n/a	n/a
9	POLR2A	chr5:96120043-96121576	U87	brain:	n/a	n/a
10	POLR2A	chr5:96120002-96121294	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr5:96120034-96122825	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:96115268..96118088-chr5:96119374..96122248,2	K562	blood:
2	chr5:96119292..96124832-chr5:96125807..96130865,7	K562	blood:
3	chr5:96118629..96120783-chr5:96140370..96143083,3	K562	blood:
4	chr5:96118629..96120777-chr5:96141002..96143083,2	K562	blood:
5	chr5:96118389..96123506-chr5:96124152..96130865,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000248734	TF binding region
ERAP1	TF binding region
ENSG00000164307	Chromatin interaction
ENSG00000272109	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]
rs27043	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]
rs27044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[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];0.95[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];0.97[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39841	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3985002	0.84[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
rs42398	ERAP1	cis	multi-tissue	Pritchard
rs42398	ERAP1	cis	lung	GTEx
rs42398	ARTS-1	cis	multi-tissue	Pritchard
rs42398	LRAP	cis	multi-tissue	Pritchard
rs42398	FAM174A	cis	cerebellum	SCAN
rs42398	ERAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs42398	ERAP1	cis	Esophagus Mucosa	GTEx
rs42398	CHD1	cis	cerebellum	SCAN
rs42398	ERAP2	cis	parietal	SCAN
rs42398	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs42398	CAST	cis	cerebellum	SCAN
rs42398	ERAP2	cis	cerebellum	SCAN
rs42398	CAST	cis	parietal	SCAN
rs42398	ERAP1	cis	Whole Blood	GTEx
rs42398	C5orf36	cis	parietal	SCAN
rs42398	ERAP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 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	chr5:96079400-96126600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:96079600-96123600	Strong transcription	Placenta	Placenta
7	chr5:96079600-96126400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:96079600-96126600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:96079600-96126600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:96092800-96126600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:96096400-96122800	Strong transcription	Primary B cells from cord blood	blood
13	chr5:96097400-96130000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr5:96097400-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr5:96097800-96126600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:96097800-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:96098000-96129600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
20	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
21	chr5:96098200-96122600	Strong transcription	Primary T cells from cord blood	blood
22	chr5:96098200-96128000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr5:96100200-96127000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:96104200-96136400	Strong transcription	Dnd41	blood
25	chr5:96104800-96126600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:96105000-96124400	Weak transcription	Aorta	Aorta
27	chr5:96105000-96127800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:96107600-96129600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:96107800-96138200	Strong transcription	GM12878-XiMat	blood
30	chr5:96108000-96129600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:96110200-96130200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:96110400-96121800	Strong transcription	Thymus	Thymus
33	chr5:96110400-96122800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:96110400-96125600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:96110600-96130400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:96111600-96126800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:96112800-96123800	Weak transcription	Brain Angular Gyrus	brain
38	chr5:96113800-96137200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:96114000-96126400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:96114400-96122600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:96114600-96120800	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:96114600-96124200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:96114600-96124200	Weak transcription	Pancreas	Pancrea
44	chr5:96114600-96124200	Weak transcription	Right Atrium	heart
45	chr5:96114600-96131000	Weak transcription	Fetal Brain Male	brain
46	chr5:96114800-96124400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:96114800-96126400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:96114800-96131200	Weak transcription	Right Ventricle	heart
49	chr5:96115000-96124200	Weak transcription	Esophagus	oesophagus
50	chr5:96115200-96121000	Weak transcription	Stomach Smooth Muscle	stomach

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