Variant report

Variant	rs6438542
Chromosome Location	chr3:119398320-119398321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:119398295-119399445	SK-N-SH	brain:	n/a	chr3:119398786-119398800 chr3:119398792-119398806

No.	Distal block	Cell Line	Cell type
1	chr3:119397978..119400630-chr3:119401218..119403216,2	MCF-7	breast:
2	chr3:119396379..119398214-chr3:119398308..119400262,2	MCF-7	breast:
3	chr3:119383346..119386464-chr3:119395342..119399056,3	K562	blood:

Variant related genes	Relation type
COX17	TF binding region
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11720605	0.83[EUR][1000 genomes]
rs11914676	0.85[JPT][hapmap]
rs11923223	0.85[JPT][hapmap]
rs13062540	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13065543	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs13065893	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1317259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830291	0.85[JPT][hapmap]
rs1872432	0.85[JPT][hapmap]
rs1880040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1880041	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046430	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2280578	0.85[JPT][hapmap]
rs2629395	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2629397	0.83[EUR][1000 genomes]
rs2629409	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2670296	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688629	0.85[JPT][hapmap]
rs2688631	0.85[JPT][hapmap]
rs2688633	0.82[EUR][1000 genomes]
rs2692618	0.88[CEU][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap]
rs2698282	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3749416	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3749417	0.92[ASN][1000 genomes]
rs3772134	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4327424	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687871	0.94[ASN][1000 genomes]
rs4688023	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4688024	0.85[JPT][hapmap]
rs484809	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs523476	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs571352	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs572119	0.84[JPT][hapmap]
rs62265884	0.83[EUR][1000 genomes]
rs6438541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6766563	0.90[JPT][hapmap]
rs6782253	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785698	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794484	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6794579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6803814	0.80[JPT][hapmap]
rs6807079	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs693397	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613999	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626940	0.90[JPT][hapmap]
rs7633444	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007	0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs940181	0.83[EUR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6438542	POPDC2	cis	lymphoblastoid	seeQTL
rs6438542	COX17	cis	lymphoblastoid	seeQTL
rs6438542	POPDC2	cis	cerebellum	SCAN
rs6438542	POPDC2	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119396600-119399000	Weak transcription	Pancreas	Pancrea
2	chr3:119396800-119398400	Weak transcription	Placenta	Placenta
3	chr3:119396800-119398600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:119396800-119400000	Weak transcription	Fetal Heart	heart
5	chr3:119397000-119398600	Weak transcription	K562	blood
6	chr3:119397000-119398800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:119397400-119398600	Weak transcription	GM12878-XiMat	blood

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