Variant report

Variant	rs9905940
Chromosome Location	chr17:46614102-46614103
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1042818	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1042822	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1123630	1.00[JPT][hapmap]
rs11868098	0.84[EUR][1000 genomes]
rs12602539	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12603976	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938390	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939811	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12946855	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12946931	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947405	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12951076	0.90[EUR][1000 genomes]
rs12952262	1.00[JPT][hapmap]
rs1529334	1.00[JPT][hapmap]
rs17703636	0.80[EUR][1000 genomes]
rs17703660	0.80[EUR][1000 genomes]
rs2202895	0.89[EUR][1000 genomes]
rs2229302	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326012	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34378400	0.84[EUR][1000 genomes]
rs35621842	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646993	1.00[JPT][hapmap]
rs4793854	0.94[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4793889	0.86[EUR][1000 genomes]
rs4793943	1.00[JPT][hapmap]
rs55859232	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56038617	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56115209	0.89[EUR][1000 genomes]
rs56128659	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62065846	0.85[EUR][1000 genomes]
rs62066689	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62066693	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504281	0.85[EUR][1000 genomes]
rs6504340	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207171	0.85[EUR][1000 genomes]
rs7222242	0.80[EUR][1000 genomes]
rs7225995	0.85[EUR][1000 genomes]
rs8064626	0.80[EUR][1000 genomes]
rs8066613	0.84[EUR][1000 genomes]
rs8071207	0.91[EUR][1000 genomes]
rs8072250	0.81[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs8073963	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8074125	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8079617	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs872760	1.00[JPT][hapmap]
rs9904760	0.81[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9906950	0.90[EUR][1000 genomes]
rs9909884	1.00[JPT][hapmap]
rs9912500	1.00[JPT][hapmap]
rs9989493	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS 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	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised 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	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription 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	349 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9905940	HOXB2	cis	Muscle Skeletal	GTEx
rs9905940	HOXB-AS1	cis	Whole Blood	GTEx
rs9905940	PNPO	cis	cerebellum	SCAN
rs9905940	KLHL11	cis	cerebellum	SCAN
rs9905940	LOC100130581	cis	parietal	SCAN
rs9905940	PYY	cis	parietal	SCAN
rs9905940	HOXB2	cis	Whole Blood	GTEx
rs9905940	HOXB2	cis	uninvolved skin	skin_eQTL
rs9905940	HOXB2	cis	cerebellum	SCAN
rs9905940	PNPO	cis	parietal	SCAN
rs9905940	PLCD3	cis	parietal	SCAN
rs9905940	PRR15L	cis	parietal	SCAN
rs9905940	HOXB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46610200-46618400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr17:46611400-46615200	Enhancers	K562	blood
3	chr17:46612200-46616400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:46613000-46614400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:46613000-46615200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr17:46613000-46615200	Enhancers	NHLF	lung
7	chr17:46613200-46615800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:46613600-46614200	Weak transcription	Fetal Kidney	kidney
9	chr17:46613800-46614200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:46613800-46614800	Weak transcription	Fetal Stomach	stomach
11	chr17:46613800-46615000	Enhancers	HSMM	muscle
12	chr17:46613800-46615400	Enhancers	A549	lung
13	chr17:46613800-46615600	Enhancers	NHDF-Ad	bronchial
14	chr17:46614000-46614200	Flanking Active TSS	NH-A	brain
15	chr17:46614000-46615000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr17:46614000-46615000	Enhancers	Hela-S3	cervix
17	chr17:46614000-46615000	Enhancers	HSMMtube	muscle

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