Variant report

Variant	rs4793846
Chromosome Location	chr17:46532906-46532907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46530850..46533321-chr17:46662351..46664282,2	K562	blood:
2	chr17:46532678..46534272-chr17:46625300..46627846,2	K562	blood:
3	chr17:46532737..46535111-chr17:46677941..46680284,2	K562	blood:
4	chr17:46532115..46533858-chr17:46568103..46570537,2	MCF-7	breast:
5	chr17:46532772..46535087-chr17:46626346..46628551,2	K562	blood:

Variant related genes	Relation type
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1027895	0.91[AFR][1000 genomes]
rs12150117	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.90[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	0.86[EUR][1000 genomes]
rs12939680	0.92[EUR][1000 genomes]
rs12940162	0.91[EUR][1000 genomes]
rs12940365	0.82[CHB][hapmap]
rs12940931	0.85[EUR][1000 genomes]
rs12941754	0.85[EUR][1000 genomes]
rs12941877	0.91[EUR][1000 genomes]
rs12943082	0.88[EUR][1000 genomes]
rs12944592	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12945780	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12945803	0.82[EUR][1000 genomes]
rs12946636	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12948017	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12948086	0.92[EUR][1000 genomes]
rs12948128	0.81[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs12950325	0.87[EUR][1000 genomes]
rs12952824	0.92[EUR][1000 genomes]
rs1396870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1533057	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]
rs1553749	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1553752	0.82[JPT][hapmap]
rs1553753	0.86[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs17621199	0.85[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs17621297	0.88[EUR][1000 genomes]
rs17621707	0.87[EUR][1000 genomes]
rs17623154	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs17623482	0.91[EUR][1000 genomes]
rs17624868	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs17694192	0.81[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs17694895	0.84[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs17696503	0.91[EUR][1000 genomes]
rs17696640	0.91[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	0.89[EUR][1000 genomes]
rs34771639	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34791545	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35003027	0.91[EUR][1000 genomes]
rs35387091	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35509644	0.91[EUR][1000 genomes]
rs35533148	0.95[EUR][1000 genomes]
rs35680046	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35759756	0.91[EUR][1000 genomes]
rs35767434	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36057069	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4128439	0.81[CEU][hapmap];0.88[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]
rs4794674	0.91[AFR][1000 genomes]
rs5000249	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs55682156	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56146024	0.94[EUR][1000 genomes]
rs56385452	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56655886	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62067799	0.86[EUR][1000 genomes]
rs6504135	0.85[EUR][1000 genomes]
rs6504145	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs6504158	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6504172	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6504257	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66529852	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206951	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs7207826	1.00[CHB][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	0.85[EUR][1000 genomes]
rs7211712	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7212149	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7212325	0.91[AFR][1000 genomes]
rs7212930	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7213513	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7214269	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7215143	0.88[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	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7218345	0.90[ASN][1000 genomes]
rs7218848	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs7219816	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7219985	0.82[JPT][hapmap]
rs7220387	0.83[AMR][1000 genomes];0.95[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[EUR][1000 genomes]
rs7224686	0.91[EUR][1000 genomes]
rs7225998	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs8065115	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs8065385	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs8067857	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8068128	0.84[CHB][hapmap]
rs8068397	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs8069900	0.87[EUR][1000 genomes]
rs8072521	0.91[EUR][1000 genomes]
rs8072770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073466	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8074054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8074443	0.84[CHB][hapmap]
rs8076655	0.85[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs8078999	0.89[EUR][1000 genomes]
rs8081754	0.83[EUR][1000 genomes]
rs9303542	0.81[CHB][hapmap]
rs9747116	0.91[AFR][1000 genomes]
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	0.82[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:2 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4793846	HOXB2	cis	Adipose Subcutaneous	GTEx
rs4793846	SKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46528800-46535200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:46529000-46535400	Enhancers	Fetal Thymus	thymus
3	chr17:46529200-46533800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46531200-46533000	Weak transcription	K562	blood
5	chr17:46531400-46533800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:46531400-46534400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:46531400-46534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr17:46531600-46533000	Enhancers	Thymus	Thymus
9	chr17:46531600-46534200	Enhancers	Primary T cells from cord blood	blood
10	chr17:46531600-46534200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:46531600-46534200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr17:46531600-46534200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr17:46531600-46534400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr17:46531600-46534400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr17:46531600-46534400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr17:46531800-46533800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:46531800-46534200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:46531800-46534200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr17:46531800-46534200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr17:46531800-46534400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr17:46532000-46535200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr17:46532200-46533000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:46532200-46534200	Weak transcription	Primary B cells from cord blood	blood
24	chr17:46532800-46533600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:46532800-46533800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr17:46532800-46534400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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