Variant report

Variant	rs6504256
Chromosome Location	chr17:46525183-46525184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46524023..46526457-chr17:46528439..46531393,2	K562	blood:
2	chr17:46518879..46521874-chr17:46522695..46525277,2	K562	blood:
3	chr17:46523948..46525611-chr17:46533793..46535794,2	K562	blood:
4	chr17:46516289..46518100-chr17:46524558..46526108,2	K562	blood:
5	chr17:46523875..46525523-chr17:46528781..46531393,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1027895	0.91[ASN][1000 genomes]
rs12942428	0.93[ASN][1000 genomes]
rs1396868	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1509635	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1553750	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1858162	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123344	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2924250	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2924254	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2938470	0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs3826397	0.93[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs4239201	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs4267363	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4606751	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs4794674	0.92[ASN][1000 genomes]
rs4794678	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504160	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs6504210	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs7209010	0.92[ASN][1000 genomes]
rs7211099	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs7211636	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7211780	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212220	0.82[ASN][1000 genomes]
rs7212325	0.91[ASN][1000 genomes]
rs7216202	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs7218287	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7221510	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs8072002	0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs8073326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073618	0.83[ASN][1000 genomes]
rs9303541	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs9747116	0.90[ASN][1000 genomes]
rs9898383	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6504256	HOXB2	cis	multi-tissue	Pritchard
rs6504256	HOXB2	cis	cerebellum	SCAN
rs6504256	PNPO	cis	parietal	SCAN
rs6504256	SOST	cis	cerebellum	SCAN
rs6504256	RAB5C	cis	parietal	SCAN
rs6504256	CDK5RAP3	cis	parietal	SCAN
rs6504256	COPZ2	cis	parietal	SCAN
rs6504256	SKAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46518800-46526200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr17:46519400-46525200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:46520600-46530800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:46522200-46525800	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr17:46522200-46526200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46522400-46525400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:46522400-46525600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:46522400-46526600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr17:46522800-46525200	Enhancers	Primary T cells from cord blood	blood
10	chr17:46523200-46527600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr17:46523400-46528800	Weak transcription	K562	blood
12	chr17:46523600-46529000	Weak transcription	Fetal Thymus	thymus
13	chr17:46523800-46528800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:46524000-46525600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr17:46524000-46527400	Weak transcription	Primary B cells from cord blood	blood
16	chr17:46524200-46527600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:46524200-46528800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:46524400-46527400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:46525000-46526000	Enhancers	Primary T cells fromperipheralblood	blood

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