Variant report

Variant	rs1714507
Chromosome Location	chr3:158251432-158251433
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1047366	0.84[ASW][hapmap];0.94[CHB][hapmap]
rs10936146	0.80[CEU][hapmap]
rs11719037	0.91[ASN][1000 genomes]
rs12107643	0.95[CHB][hapmap]
rs12637678	1.00[ASN][1000 genomes]
rs12638438	0.90[ASN][1000 genomes]
rs13074694	0.95[CHB][hapmap];0.80[GIH][hapmap]
rs1435641	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1435642	0.84[ASW][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap]
rs1435643	0.80[CHB][hapmap]
rs1595028	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1595029	0.99[ASN][1000 genomes]
rs1620229	0.80[AFR][1000 genomes]
rs1656365	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1656366	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1656373	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1656374	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1656376	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1656377	0.95[CHB][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs1714516	0.80[AFR][1000 genomes]
rs1714518	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1714524	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17629390	0.94[CHB][hapmap];0.90[YRI][hapmap]
rs17630086	0.80[CHB][hapmap]
rs1836688	0.84[ASW][hapmap];0.95[CHB][hapmap];0.90[YRI][hapmap]
rs1864507	0.95[CHB][hapmap]
rs1978779	0.82[JPT][hapmap]
rs2303909	0.84[ASW][hapmap];0.95[CHB][hapmap]
rs2364274	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs2731112	1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs2731120	0.80[AFR][1000 genomes]
rs2731122	0.80[AFR][1000 genomes]
rs3765025	0.95[CHB][hapmap];0.90[YRI][hapmap]
rs4680445	0.90[YRI][hapmap]
rs4875	0.84[ASW][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap]
rs6441206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6762860	0.91[ASN][1000 genomes]
rs6772483	0.84[ASW][hapmap];0.95[CHB][hapmap]
rs6774461	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs6787172	0.96[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6795376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6800914	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs6803047	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs6804259	0.95[CHB][hapmap];0.85[YRI][hapmap]
rs7612250	0.80[CHB][hapmap]
rs7613814	0.89[CHB][hapmap];0.95[YRI][hapmap]
rs7613824	0.80[CHB][hapmap]
rs7620927	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs7621897	0.95[CHB][hapmap]
rs7623732	0.91[ASN][1000 genomes]
rs7628293	0.80[CHB][hapmap]
rs7631310	0.84[ASW][hapmap];0.95[CHB][hapmap];0.90[YRI][hapmap]
rs7639678	0.99[ASN][1000 genomes]
rs7648618	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs827106	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs827135	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs8455	0.95[CHB][hapmap]
rs891464	0.84[ASW][hapmap];0.95[CHB][hapmap]
rs9810114	0.86[JPT][hapmap]
rs9810887	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9819134	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9819567	0.95[CHB][hapmap]
rs9857535	0.92[ASN][1000 genomes]
rs9858318	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs9859129	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs9883657	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1014557	chr3:158176582-158251602	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1714507	LXN	cis	lymphoblastoid	seeQTL
rs1714507	RP11-538P18.2	cis	Artery Tibial	GTEx
rs1714507	VEPH1	cis	cerebellum	SCAN
rs1714507	BRD7	cis	cerebellum	SCAN
rs1714507	RSRC1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158246600-158261000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr3:158249400-158264400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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