Variant report

Variant	rs17270169
Chromosome Location	chr19:42673597-42673598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42652766..42655502-chr19:42672644..42674234,2	MCF-7	breast:
2	chr19:42671890..42674434-chr19:42677210..42680964,4	K562	blood:
3	chr19:42662242..42664817-chr19:42671990..42673676,2	MCF-7	breast:
4	chr19:42672373..42674128-chr19:42703311..42705172,2	K562	blood:
5	chr19:42673347..42674972-chr19:42675529..42678230,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000028277	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10407506	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10500285	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878620	0.86[GIH][hapmap]
rs11878917	0.91[AMR][1000 genomes]
rs11880124	0.85[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs11883412	0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12232804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16975663	0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs16975684	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs17270057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17342067	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17342179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17342284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17750207	0.80[AMR][1000 genomes]
rs2217342	0.87[TSI][hapmap]
rs2302485	0.86[GIH][hapmap];1.00[YRI][hapmap]
rs2303652	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs3736109	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs3745231	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs3745233	0.85[CHB][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs3810148	1.00[YRI][hapmap]
rs3810151	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs3826705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4141062	0.86[GIH][hapmap];1.00[YRI][hapmap]
rs443239	0.90[CEU][hapmap];0.93[CHD][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs454150	0.81[CEU][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs4803520	0.90[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs7248379	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7251466	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes]
rs7253767	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7253791	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7253915	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs741070	1.00[YRI][hapmap]
rs8106871	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8182491	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs899661	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active 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	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17270169	ZNF219	trans	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42657400-42676400	Weak transcription	Gastric	stomach
2	chr19:42664600-42674600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:42664600-42674600	Weak transcription	Fetal Brain Female	brain
4	chr19:42670400-42673800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:42670600-42673800	Weak transcription	Fetal Brain Male	brain
6	chr19:42671000-42675200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42672000-42677400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:42672800-42676000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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