Variant report

Variant	rs27529
Chromosome Location	chr5:96126308-96126309
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	chr5:96126208-96127642	U87	brain:	n/a	n/a
2	POLR2A	chr5:96126152-96127648	U87	brain:	n/a	n/a
3	POLR2A	chr5:96123725-96127973	A549	lung:	n/a	n/a
4	POLR2A	chr5:96125389-96127158	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96119292..96124832-chr5:96125807..96130865,7	K562	blood:
2	chr5:96118389..96123506-chr5:96124152..96130865,8	K562	blood:
3	chr5:96125291..96127024-chr5:96141559..96143883,2	K562	blood:

Variant related genes	Relation type
ERAP1	TF binding region
ENSG00000248734	Chromatin interaction
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs149189	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs151823	0.87[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs151940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs151964	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152280	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs152466	0.81[ASN][1000 genomes]
rs152468	0.87[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs168674	0.84[AMR][1000 genomes]
rs173491	0.81[JPT][hapmap]
rs184971	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs187387	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs190298	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs246453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246454	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246455	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246456	0.88[AMR][1000 genomes]
rs2549805	0.87[CHB][hapmap]
rs26489	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs26490	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs26491	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs26493	0.87[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs26495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs26496	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs26497	0.99[ASN][1000 genomes]
rs26498	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs26499	0.85[JPT][hapmap];0.92[YRI][hapmap]
rs26500	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs26510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26512	0.99[ASN][1000 genomes]
rs26653	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs26654	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs26655	0.89[ASN][1000 genomes]
rs27043	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs27044	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs27045	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs27432	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs27434	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.99[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs27527	0.83[ASN][1000 genomes]
rs27640	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs27645	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs27694	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs27710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28333	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28337	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs30185	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs30186	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs30187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30334	0.87[ASN][1000 genomes]
rs30376	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs30378	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34735	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs34737	0.81[ASN][1000 genomes]
rs34750	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs34751	0.88[ASN][1000 genomes]
rs34752	0.87[ASN][1000 genomes]
rs39840	0.83[ASN][1000 genomes]
rs39841	0.82[ASN][1000 genomes]
rs42398	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs467735	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs469367	0.89[ASN][1000 genomes]
rs469674	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs469758	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469783	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs695965	0.88[ASN][1000 genomes]
rs845028	0.87[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs27529	ERAP2	cis	parietal	SCAN
rs27529	ARTS-1	cis	multi-tissue	Pritchard
rs27529	LRAP	cis	multi-tissue	Pritchard
rs27529	ERAP2	cis	cerebellum	SCAN
rs27529	ERAP1	cis	multi-tissue	Pritchard
rs27529	ERAP2	cis	lymphoblastoid	seeQTL
rs27529	C5orf27	cis	parietal	SCAN
rs27529	ERAP1	cis	lung	GTEx
rs27529	ERAP1	cis	Muscle Skeletal	GTEx
rs27529	ERAP1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:96068600-96130000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:96071400-96126600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:96079400-96126600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:96079600-96126400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:96079600-96126600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:96079600-96126600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:96092800-96126600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:96097400-96130000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr5:96097400-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr5:96097800-96126600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:96097800-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:96098000-96129600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
17	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
18	chr5:96098200-96128000	Strong transcription	Primary hematopoietic stem cells	blood
19	chr5:96100200-96127000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:96104200-96136400	Strong transcription	Dnd41	blood
21	chr5:96104800-96126600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:96105000-96127800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:96107600-96129600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:96107800-96138200	Strong transcription	GM12878-XiMat	blood
25	chr5:96108000-96129600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:96110200-96130200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:96110600-96130400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:96111600-96126800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:96113800-96137200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:96114000-96126400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:96114600-96131000	Weak transcription	Fetal Brain Male	brain
32	chr5:96114800-96126400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:96114800-96131200	Weak transcription	Right Ventricle	heart
34	chr5:96115200-96141200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:96115400-96142000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:96116000-96126400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:96116000-96126600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:96116200-96141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:96117000-96126600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:96117200-96126400	Weak transcription	HSMMtube	muscle
41	chr5:96117400-96137000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:96117600-96131800	Strong transcription	Liver	Liver
43	chr5:96118600-96126400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:96118600-96126800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:96118800-96126400	Strong transcription	Fetal Intestine Large	intestine
46	chr5:96118800-96126600	Weak transcription	NH-A	brain
47	chr5:96119000-96126600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:96119000-96126600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:96119000-96130800	Weak transcription	Psoas Muscle	Psoas
50	chr5:96119000-96142000	Weak transcription	A549	lung

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