Variant report

Variant	rs245442
Chromosome Location	chr7:80917148-80917149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1012950	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1012951	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1015885	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10235727	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10244235	0.84[ASN][1000 genomes]
rs10254060	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10259342	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486817	0.93[ASN][1000 genomes]
rs10954564	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12155276	0.82[ASN][1000 genomes]
rs12531400	0.83[ASN][1000 genomes]
rs12535166	0.83[ASN][1000 genomes]
rs12707314	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13228901	0.82[ASN][1000 genomes]
rs1397005	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1509913	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs161828	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs161829	0.84[ASN][1000 genomes]
rs161830	0.84[ASN][1000 genomes]
rs161831	0.85[ASN][1000 genomes]
rs161832	0.84[ASN][1000 genomes]
rs161833	0.85[ASN][1000 genomes]
rs161834	0.84[ASN][1000 genomes]
rs161835	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs161836	0.85[ASN][1000 genomes]
rs161837	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs161838	0.84[ASN][1000 genomes]
rs161839	0.84[ASN][1000 genomes]
rs161840	0.85[ASN][1000 genomes]
rs161841	0.85[ASN][1000 genomes]
rs161842	0.85[ASN][1000 genomes]
rs161843	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs161845	0.85[ASN][1000 genomes]
rs161847	0.84[ASN][1000 genomes]
rs161848	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs161849	0.84[ASN][1000 genomes]
rs162133	0.84[ASN][1000 genomes]
rs162134	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs162136	0.84[ASN][1000 genomes]
rs162137	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs17626401	0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2040901	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs2057776	0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2107392	0.84[ASN][1000 genomes]
rs2189557	0.82[ASN][1000 genomes]
rs2189558	0.82[ASN][1000 genomes]
rs2189559	0.83[ASN][1000 genomes]
rs2189565	0.88[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2214549	0.82[ASN][1000 genomes]
rs2367489	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs245415	0.84[ASN][1000 genomes]
rs245416	0.84[ASN][1000 genomes]
rs245417	0.85[ASN][1000 genomes]
rs245418	0.85[ASN][1000 genomes]
rs245419	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs245421	0.84[ASN][1000 genomes]
rs245422	0.85[ASN][1000 genomes]
rs245423	0.84[ASN][1000 genomes]
rs245424	0.85[ASN][1000 genomes]
rs245425	0.84[ASN][1000 genomes]
rs245426	0.85[ASN][1000 genomes]
rs245430	0.84[ASN][1000 genomes]
rs245433	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245434	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245436	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245439	0.88[ASN][1000 genomes]
rs245440	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245441	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2886992	0.91[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325966	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs325967	0.82[ASN][1000 genomes]
rs325971	0.85[ASN][1000 genomes]
rs325972	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs325973	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs325974	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs325975	0.84[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs325976	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs34356376	0.80[ASN][1000 genomes]
rs34813026	0.82[ASN][1000 genomes]
rs35177237	0.84[ASN][1000 genomes]
rs4728387	0.83[ASN][1000 genomes]
rs4732201	0.83[ASN][1000 genomes]
rs4732204	0.83[ASN][1000 genomes]
rs4732211	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4732237	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs60216102	0.85[ASN][1000 genomes]
rs62465492	0.99[ASN][1000 genomes]
rs6943816	0.80[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6947842	0.82[ASN][1000 genomes]
rs6948864	0.82[ASN][1000 genomes]
rs6950573	0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6962364	0.80[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6965375	0.83[ASN][1000 genomes]
rs7455237	0.82[ASN][1000 genomes]
rs7784690	0.84[ASN][1000 genomes]
rs7803017	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs976328	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs995353	0.80[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv831044	chr7:80721773-80918591	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv888557	chr7:80813081-80917148	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1023149	chr7:80817550-80928090	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv888558	chr7:80844667-80917148	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv607686	chr7:80857196-80917148	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv888559	chr7:80870379-80917148	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs245442	PHTF2	cis	cerebellum	SCAN
rs245442	CD36	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80913200-80928800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:80914400-80928000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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