Variant report

Variant	rs35621842
Chromosome Location	chr17:46606222-46606223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46605320..46607362-chr17:46701075..46703388,2	K562	blood:
2	chr17:46605844..46607979-chr17:46670132..46672345,2	K562	blood:
3	chr17:46599448..46601995-chr17:46604125..46606686,2	MCF-7	breast:
4	chr17:46582615..46585067-chr17:46605741..46607260,2	MCF-7	breast:
5	chr17:46597156..46601458-chr17:46601809..46606314,7	MCF-7	breast:
6	chr17:46568782..46571366-chr17:46604713..46607657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120075	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1042818	0.93[EUR][1000 genomes]
rs1042822	0.93[EUR][1000 genomes]
rs1123630	0.80[CEU][hapmap]
rs11868098	0.92[EUR][1000 genomes]
rs12602539	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12603976	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12938390	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12939811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946855	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12946931	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12947405	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12951076	0.92[EUR][1000 genomes]
rs17703636	0.91[EUR][1000 genomes]
rs17703660	0.91[EUR][1000 genomes]
rs2202895	0.87[EUR][1000 genomes]
rs2229302	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2326012	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34378400	0.95[EUR][1000 genomes]
rs4793854	0.82[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4793889	0.94[EUR][1000 genomes]
rs4793943	0.80[CEU][hapmap]
rs55859232	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56038617	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56115209	0.91[EUR][1000 genomes]
rs56128659	0.95[EUR][1000 genomes]
rs62065846	0.96[EUR][1000 genomes]
rs62066689	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62066693	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6504281	0.84[EUR][1000 genomes]
rs6504340	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];0.83[ASN][1000 genomes]
rs7207109	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207171	0.84[EUR][1000 genomes]
rs7222242	0.91[EUR][1000 genomes]
rs7225995	0.96[EUR][1000 genomes]
rs8064626	0.91[EUR][1000 genomes]
rs8066613	0.95[EUR][1000 genomes]
rs8071207	0.88[EUR][1000 genomes]
rs8072250	0.93[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs8073963	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8074125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8079617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872760	0.80[CEU][hapmap]
rs9904760	0.93[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs9905940	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9906950	0.88[EUR][1000 genomes]
rs9989493	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs35621842	NBR1	cis	parietal	SCAN
rs35621842	HOXB2	cis	cerebellum	SCAN
rs35621842	HOXB2	cis	Adipose Subcutaneous	GTEx
rs35621842	HOXB-AS1	cis	Whole Blood	GTEx
rs35621842	PNPO	cis	cerebellum	SCAN
rs35621842	LOC100130581	cis	parietal	SCAN
rs35621842	KLHL11	cis	cerebellum	SCAN
rs35621842	PYY	cis	parietal	SCAN
rs35621842	HOXB2	cis	Whole Blood	GTEx
rs35621842	PNPO	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46603600-46609000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr17:46603600-46609200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:46605000-46606600	Bivalent Enhancer	Fetal Stomach	stomach
4	chr17:46605000-46607000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:46605000-46610000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr17:46605200-46606400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:46605200-46606400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
8	chr17:46605200-46606400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:46605200-46606600	Enhancers	Fetal Kidney	kidney
10	chr17:46605200-46613000	Weak transcription	NHLF	lung
11	chr17:46605400-46607400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr17:46605400-46607800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:46605600-46606400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
14	chr17:46605600-46606600	Enhancers	HSMMtube	muscle
15	chr17:46605600-46606600	Enhancers	K562	blood
16	chr17:46605800-46606400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr17:46605800-46607000	Enhancers	NHEK	skin
18	chr17:46605800-46609800	Weak transcription	Right Atrium	heart
19	chr17:46606000-46606400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr17:46606000-46607400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
21	chr17:46606000-46607400	Bivalent Enhancer	Placenta	Placenta
22	chr17:46606000-46607800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:46606200-46606400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:46606200-46607000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
25	chr17:46606200-46609200	Weak transcription	A549	lung

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