Variant report

Variant	rs2189565
Chromosome Location	chr7:80937733-80937734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:80547316..80550136-chr7:80937588..80939267,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075223	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1012950	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1012951	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1015885	0.87[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10215927	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10235727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10254060	0.80[JPT][hapmap]
rs10259342	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10270613	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10486817	0.99[ASN][1000 genomes]
rs10954564	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12707314	0.84[CHD][hapmap];0.80[JPT][hapmap]
rs1397005	0.84[CHD][hapmap]
rs1509913	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs161828	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs161835	0.80[JPT][hapmap]
rs161837	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs161843	0.84[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap]
rs161848	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs162134	0.80[JPT][hapmap]
rs162137	0.80[JPT][hapmap]
rs17626401	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2040901	0.91[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2057776	0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2367489	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs245419	0.80[JPT][hapmap]
rs245433	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs245434	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs245436	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs245439	0.82[ASN][1000 genomes]
rs245440	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs245441	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs245442	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2886992	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs325966	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs325972	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs325974	0.80[JPT][hapmap]
rs35177237	0.82[ASN][1000 genomes]
rs3948712	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4732211	0.80[JPT][hapmap]
rs4732237	0.87[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs62465492	0.93[ASN][1000 genomes]
rs6943816	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6947842	0.88[ASN][1000 genomes]
rs6948864	0.88[ASN][1000 genomes]
rs6950573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6962364	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7794553	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7803017	0.80[JPT][hapmap]
rs976328	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs995353	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034690	chr7:80520004-80987682	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1029034	chr7:80838012-81137146	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv831045	chr7:80841693-81012404	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv464608	chr7:80866153-80938045	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv607687	chr7:80866153-80938045	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv607688	chr7:80870379-80947517	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2189565	PHTF2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80929400-80938000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:80929800-80938000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:80930000-80937800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:80930000-80937800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:80930000-80937800	Weak transcription	NHLF	lung
6	chr7:80930000-80938200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:80930000-80961000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:80930200-80937800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:80930400-80938000	Weak transcription	A549	lung
10	chr7:80932800-80938000	Weak transcription	Fetal Intestine Large	intestine
11	chr7:80934200-80937800	Weak transcription	Stomach Mucosa	stomach
12	chr7:80937400-80938200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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