Variant report

Variant	rs17619124
Chromosome Location	chr7:12853902-12853903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:12853166..12855784-chr7:12857906..12859818,2	K562	blood:
2	chr7:12853864..12855585-chr7:12855723..12857729,3	K562	blood:
3	chr7:12844977..12847724-chr7:12851734..12854680,3	K562	blood:
4	chr7:12847834..12849363-chr7:12852693..12855158,2	K562	blood:
5	chr7:12757666..12759532-chr7:12853077..12856020,2	K562	blood:
6	chr7:12848902..12851417-chr7:12852205..12854551,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10229134	0.82[EUR][1000 genomes]
rs10230511	1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs10238211	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10238367	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10240689	0.90[ASN][1000 genomes]
rs10243288	0.90[EUR][1000 genomes]
rs10243324	0.86[EUR][1000 genomes]
rs10246359	0.82[EUR][1000 genomes]
rs10254295	0.96[ASN][1000 genomes]
rs10259240	0.94[ASN][1000 genomes]
rs10259524	0.96[ASN][1000 genomes]
rs10269634	0.87[EUR][1000 genomes]
rs10278442	0.89[EUR][1000 genomes]
rs17166415	0.97[ASN][1000 genomes]
rs17166416	0.96[ASN][1000 genomes]
rs17619332	0.90[EUR][1000 genomes]
rs17681457	0.94[ASN][1000 genomes]
rs1990346	0.82[EUR][1000 genomes]
rs2109290	0.87[EUR][1000 genomes]
rs2191265	0.93[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs2191266	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs2215333	0.88[EUR][1000 genomes]
rs2356698	0.97[ASN][1000 genomes]
rs2357046	0.92[ASN][1000 genomes]
rs2357049	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2357052	0.89[CEU][hapmap]
rs2357053	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs28433921	0.88[EUR][1000 genomes]
rs28873158	0.94[ASN][1000 genomes]
rs35490471	0.82[EUR][1000 genomes]
rs4288267	0.82[EUR][1000 genomes]
rs4288268	0.90[ASN][1000 genomes]
rs4480006	0.82[ASN][1000 genomes]
rs4719339	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs4721148	0.87[CHB][hapmap]
rs4721153	0.96[CEU][hapmap]
rs55991971	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56082010	0.82[ASN][1000 genomes]
rs6460980	0.94[ASN][1000 genomes]
rs6942839	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6948718	0.88[EUR][1000 genomes]
rs6950280	0.86[EUR][1000 genomes]
rs6950340	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs6953097	0.86[EUR][1000 genomes]
rs6961897	0.86[EUR][1000 genomes]
rs6962633	0.81[EUR][1000 genomes]
rs6969461	0.88[EUR][1000 genomes]
rs6976082	0.88[EUR][1000 genomes]
rs758675	0.93[CEU][hapmap]
rs7783477	0.94[ASN][1000 genomes]
rs7787728	0.90[ASN][1000 genomes]
rs7790527	0.86[EUR][1000 genomes]
rs7791902	0.96[ASN][1000 genomes]
rs7793747	0.80[ASN][1000 genomes]
rs7800218	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs7800580	0.82[EUR][1000 genomes]
rs7803338	0.88[EUR][1000 genomes]
rs7808814	0.90[ASN][1000 genomes]
rs7809081	0.82[EUR][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	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	esv2422346	chr7:12739291-12883550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1027501	chr7:12743592-12927109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1020568	chr7:12802640-13183737	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027806	chr7:12842708-12875714	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	nsv1016775	chr7:12845004-12865643	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
12	nsv981801	chr7:12848501-12854945	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17619124	PHEX	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12845800-12854400	Weak transcription	K562	blood
2	chr7:12846800-12854800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:12849600-12854400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:12850000-12856800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:12853200-12854800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:12853200-12854800	Enhancers	HMEC	breast
7	chr7:12853200-12855200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:12853600-12854000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:12853600-12854400	Flanking Active TSS	NHEK	skin
10	chr7:12853800-12854200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:12853800-12854600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr7:12853800-12857200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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