Variant report

Variant	rs1082502
Chromosome Location	chr12:58035706-58035707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10082911	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10083154	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10783836	0.92[EUR][1000 genomes]
rs10783842	0.89[EUR][1000 genomes]
rs10783843	0.84[EUR][1000 genomes]
rs10783844	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1082503	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876993	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10877001	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877006	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877007	0.94[EUR][1000 genomes]
rs10877008	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1092472	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172277	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172306	0.93[EUR][1000 genomes]
rs11533604	0.80[ASN][1000 genomes]
rs12302351	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12302451	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12314562	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12316021	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12809742	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1585781	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1628552	0.87[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes]
rs1629032	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1633360	0.80[ASN][1000 genomes]
rs1678504	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1678505	0.89[EUR][1000 genomes]
rs1678511	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678512	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678513	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678515	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678519	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1678520	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678522	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678527	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1678528	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1678529	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1678530	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678531	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678532	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678534	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678539	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678540	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1689584	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1689585	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1689586	0.95[EUR][1000 genomes]
rs1689592	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1689594	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1689595	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1689596	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1689597	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1689600	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1689601	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1689603	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1689604	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1871417	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2169987	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2277322	0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs238516	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs2619441	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2619466	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2640629	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap]
rs2640630	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2640631	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2928053	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2928054	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2928055	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2928061	0.95[EUR][1000 genomes]
rs2928062	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2928064	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3825078	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760164	0.95[EUR][1000 genomes]
rs4760165	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760168	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs701006	0.86[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs703832	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7136269	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314152	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs774887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs774888	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774890	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap]
rs774891	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7976852	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs7979246	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs799575	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs810204	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv511490	chr12:58026786-58035706	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	esv1802058	chr12:58028127-58062667	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
6	nsv559044	chr12:58028671-58065448	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	nsv975499	chr12:58034418-58068937	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1082502	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1082502	NXPH4	cis	cerebellum	SCAN
rs1082502	TSPAN31	cis	parietal	SCAN
rs1082502	DKFZP586D0919	cis	multi-tissue	Pritchard
rs1082502	KRT75	cis	cerebellum	SCAN
rs1082502	FAM119B	cis	lymphoblastoid	seeQTL
rs1082502	CDK4	cis	cerebellum	SCAN
rs1082502	CDK2	cis	parietal	SCAN
rs1082502	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1082502	ITGB7	cis	cerebellum	SCAN
rs1082502	STAT6	cis	cerebellum	SCAN
rs1082502	HSD17B6	cis	cerebellum	SCAN
rs1082502	SLC26A10	cis	Heart Left Ventricle	GTEx
rs1082502	FAM119B	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58032600-58036000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:58034800-58036600	Enhancers	K562	blood
3	chr12:58035000-58035800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr12:58035200-58036000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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