Variant report

Variant	rs245436
Chromosome Location	chr7:80912415-80912416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1012950	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1012951	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1015885	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10235727	0.87[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10254060	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10259342	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10486817	0.82[ASN][1000 genomes]
rs10954564	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12707314	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs1397005	0.85[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs1509913	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs161828	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs161835	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs161837	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs161843	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs161848	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs162134	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs162137	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs17626401	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2040901	0.80[GIH][hapmap]
rs2057776	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2189565	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2367489	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs245419	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs245433	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245434	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245439	0.82[ASN][1000 genomes]
rs245440	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs245441	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs245442	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2886992	0.83[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs325966	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs325972	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs325973	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs325974	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs325975	0.84[CHB][hapmap]
rs325976	0.86[CHB][hapmap]
rs4732211	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4732237	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs62465492	0.88[ASN][1000 genomes]
rs6943816	0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs6950573	0.87[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6962364	0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs7803017	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs976328	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs995353	0.80[CHB][hapmap];0.85[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs245436	PHTF2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80910200-80912800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:80910200-80912800	Weak transcription	NHEK	skin
3	chr7:80910200-80913000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:80910400-80913000	Weak transcription	HSMM	muscle
5	chr7:80910600-80913000	Weak transcription	HMEC	breast

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