Variant report

Variant	rs1533057
Chromosome Location	chr17:46519105-46519106
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46519089..46520799-chr17:46536940..46538843,2	K562	blood:
2	chr17:46518879..46521874-chr17:46522695..46525277,2	K562	blood:
3	chr17:46511985..46515396-chr17:46515822..46520337,5	K562	blood:
4	chr17:46517956..46520413-chr17:46654283..46656139,2	K562	blood:

Variant related genes	Relation type
ENSG00000264451	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs12150117	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs12449653	0.84[CHB][hapmap]
rs12450081	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs12452212	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12938032	0.88[EUR][1000 genomes]
rs12939680	0.94[EUR][1000 genomes]
rs12940162	0.92[EUR][1000 genomes]
rs12940365	0.82[CHB][hapmap]
rs12940931	0.87[EUR][1000 genomes]
rs12941754	0.87[EUR][1000 genomes]
rs12941877	0.92[EUR][1000 genomes]
rs12943082	0.89[EUR][1000 genomes]
rs12944592	0.84[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs12945780	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12945803	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12946636	0.84[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs12948017	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12948086	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12948128	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs12950325	0.89[EUR][1000 genomes]
rs12952824	0.93[EUR][1000 genomes]
rs1396870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553749	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1553752	0.82[JPT][hapmap]
rs1553753	0.85[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs17621199	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs17621297	0.89[EUR][1000 genomes]
rs17621707	0.88[EUR][1000 genomes]
rs17623154	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs17623482	0.92[EUR][1000 genomes]
rs17624868	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs17694192	0.85[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs17694895	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs17696503	0.92[EUR][1000 genomes]
rs17696640	0.92[EUR][1000 genomes]
rs17697950	1.00[CHB][hapmap]
rs1912154	0.82[JPT][hapmap]
rs2056458	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2084881	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2175158	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs34466582	0.91[EUR][1000 genomes]
rs34771639	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34791545	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35003027	0.92[EUR][1000 genomes]
rs35387091	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35509644	0.92[EUR][1000 genomes]
rs35533148	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35680046	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713035	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35759756	0.92[EUR][1000 genomes]
rs35767434	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36057069	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4128439	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs4261589	0.90[ASN][1000 genomes]
rs4312351	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4451990	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4556829	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4793846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5000249	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs55682156	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56146024	0.95[EUR][1000 genomes]
rs56385452	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56655886	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62067799	0.88[EUR][1000 genomes]
rs6504135	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs6504145	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs6504158	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6504172	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6504257	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66529852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206951	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7207826	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7209043	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7209855	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7210708	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7211607	0.87[EUR][1000 genomes]
rs7211712	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7212149	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7212930	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7213513	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7214269	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7215143	0.89[EUR][1000 genomes]
rs7216971	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7217025	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7217120	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7218217	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7218345	0.90[ASN][1000 genomes]
rs7218848	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs7219816	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7219985	0.82[JPT][hapmap]
rs7220387	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7221770	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7222452	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7222593	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs7224686	0.92[EUR][1000 genomes]
rs7225998	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs8065115	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs8065385	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs8067857	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8068128	0.83[CHB][hapmap]
rs8068397	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs8069900	0.88[EUR][1000 genomes]
rs8072521	0.92[EUR][1000 genomes]
rs8072770	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073466	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8074054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8074443	0.84[CHB][hapmap]
rs8076655	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs8078999	0.91[EUR][1000 genomes]
rs8081754	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs9303542	0.81[CHB][hapmap]
rs9891073	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9891635	0.90[ASN][1000 genomes]
rs9894812	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9897162	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9897588	0.89[ASN][1000 genomes]
rs9898988	0.87[ASN][1000 genomes]
rs9900511	0.90[ASN][1000 genomes]
rs9905961	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9906193	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9907699	0.81[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9909002	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9909872	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9910535	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9916227	0.84[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv2761960	chr17:46504489-46529846	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1533057	PNPO	cis	cerebellum	SCAN
rs1533057	PNPO	cis	parietal	SCAN
rs1533057	SKAP1	Cis_1M	lymphoblastoid	RTeQTL
rs1533057	HOXB2	cis	cerebellum	SCAN
rs1533057	HOXB6	cis	cerebellum	SCAN
rs1533057	HOXB2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46510600-46524000	Enhancers	Primary T cells fromperipheralblood	blood
2	chr17:46512600-46524200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr17:46513600-46523800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:46513800-46520800	Enhancers	Fetal Thymus	thymus
5	chr17:46514800-46522000	Enhancers	Primary B cells from peripheral blood	blood
6	chr17:46515400-46520600	Enhancers	Primary hematopoietic stem cells	blood
7	chr17:46515400-46522800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr17:46515600-46520600	Enhancers	Thymus	Thymus
9	chr17:46515800-46522600	Enhancers	K562	blood
10	chr17:46515800-46524000	Enhancers	Primary B cells from cord blood	blood
11	chr17:46516000-46519600	Enhancers	Duodenum Mucosa	Duodenum
12	chr17:46516600-46520600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:46517200-46520600	Enhancers	Dnd41	blood
14	chr17:46517400-46520400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:46517800-46521800	Weak transcription	Gastric	stomach
16	chr17:46518200-46519200	Weak transcription	Fetal Kidney	kidney
17	chr17:46518200-46519200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr17:46518400-46519400	Bivalent Enhancer	Fetal Lung	lung
19	chr17:46518600-46519200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr17:46518600-46520800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:46518600-46522000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr17:46518800-46519200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
23	chr17:46518800-46519600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr17:46518800-46520200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr17:46518800-46526200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr17:46519000-46519200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:46519000-46519200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:46519000-46519200	Enhancers	Spleen	Spleen
29	chr17:46519000-46519400	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr17:46519000-46519400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr17:46519000-46519400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:46519000-46519600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr17:46519000-46519600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr17:46519000-46519800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr17:46519000-46519800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr17:46519000-46520000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr17:46519000-46520200	Flanking Active TSS	GM12878-XiMat	blood
38	chr17:46519000-46520400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:46519000-46520600	Weak transcription	Adipose Nuclei	Adipose
40	chr17:46519000-46521800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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