Variant report

Variant	rs1925921
Chromosome Location	chr6:109847028-109847029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109804079..109806349-chr6:109846608..109849218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112365	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10872041	0.82[EUR][1000 genomes]
rs10872052	0.81[CEU][hapmap]
rs1096136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096138	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753828	0.81[EUR][1000 genomes]
rs11754263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966009	0.81[EUR][1000 genomes]
rs11968485	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs12200787	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12215867	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs12524352	0.82[CEU][hapmap]
rs1321327	0.80[CEU][hapmap]
rs1358759	0.85[EUR][1000 genomes]
rs1406957	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs1474959	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs1570011	0.81[EUR][1000 genomes]
rs1570013	0.81[CEU][hapmap]
rs1590187	0.85[EUR][1000 genomes]
rs17540056	0.81[EUR][1000 genomes]
rs1985123	0.85[EUR][1000 genomes]
rs1998812	0.84[EUR][1000 genomes]
rs2016207	0.81[CEU][hapmap]
rs2064820	0.82[EUR][1000 genomes]
rs2064822	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145144	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2232448	0.95[MKK][hapmap];0.83[YRI][hapmap]
rs2357123	0.82[EUR][1000 genomes]
rs2357127	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357128	0.83[TSI][hapmap]
rs4296926	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4523125	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs4946982	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946986	0.82[EUR][1000 genomes]
rs4946987	0.82[EUR][1000 genomes]
rs4946992	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs4946995	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946997	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947004	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.86[EUR][1000 genomes]
rs56264193	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437563	0.81[EUR][1000 genomes]
rs6568578	1.00[CHB][hapmap]
rs6568579	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6568580	0.85[EUR][1000 genomes]
rs6568582	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6568583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568595	0.81[CEU][hapmap]
rs6568601	0.81[EUR][1000 genomes]
rs6900133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900187	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911851	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6912368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6916239	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6917300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	0.81[CEU][hapmap]
rs6924436	0.83[EUR][1000 genomes]
rs6925886	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929823	0.81[EUR][1000 genomes]
rs6931630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6938741	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6942171	0.81[EUR][1000 genomes]
rs7450970	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7453835	0.80[CEU][hapmap]
rs7744981	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7745469	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7749910	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7761008	0.80[CEU][hapmap]
rs7769789	1.00[CHB][hapmap]
rs7771729	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7772109	0.82[EUR][1000 genomes]
rs7773915	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7775420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829816	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs829817	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320290	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320294	0.80[EUR][1000 genomes]
rs9320295	0.81[EUR][1000 genomes]
rs9320296	0.81[EUR][1000 genomes]
rs9320299	0.81[EUR][1000 genomes]
rs9320300	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320303	1.00[CEU][hapmap]
rs9320304	0.80[CEU][hapmap]
rs9372220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372221	0.80[CEU][hapmap]
rs9372222	0.81[CEU][hapmap]
rs9374092	0.85[EUR][1000 genomes]
rs9374095	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs9374096	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374097	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9374098	0.80[EUR][1000 genomes]
rs9374099	0.82[EUR][1000 genomes]
rs9374108	0.80[CEU][hapmap]
rs9384713	0.82[EUR][1000 genomes]
rs9384715	0.81[EUR][1000 genomes]
rs9384717	0.83[TSI][hapmap]
rs9386812	0.82[EUR][1000 genomes]
rs9386813	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9386814	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386824	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9398204	0.83[EUR][1000 genomes]
rs9400289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400291	0.82[EUR][1000 genomes]
rs9400294	0.82[EUR][1000 genomes]
rs9400295	0.82[EUR][1000 genomes]
rs9400300	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400310	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs9400312	0.81[CEU][hapmap]
rs9400316	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs942923	0.83[EUR][1000 genomes]
rs942924	0.84[EUR][1000 genomes]
rs9480973	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs9480974	0.82[EUR][1000 genomes]
rs9480976	0.82[EUR][1000 genomes]
rs9480984	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9480991	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9487141	0.82[EUR][1000 genomes]
rs9487148	0.82[EUR][1000 genomes]
rs9487171	0.81[CEU][hapmap]
rs9487172	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9487175	0.81[CEU][hapmap]
rs9487176	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9487180	0.81[CEU][hapmap]
rs971432	0.81[CEU][hapmap]
rs9968792	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9986507	0.81[CEU][hapmap];0.85[TSI][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1925921	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs1925921	AKD1	cis	lymphoblastoid	seeQTL
rs1925921	FIG4	cis	cerebellum	SCAN
rs1925921	SMPD2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109835400-109851400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:109838600-109861400	Weak transcription	Thymus	Thymus
3	chr6:109839000-109848200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:109845400-109851000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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