Variant report

Variant	rs9400289
Chromosome Location	chr6:109847992-109847993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109847963..109848914-chr6:110104179..110105102,2	K562	blood:
2	chr6:109847935..109850549-chr6:110011645..110013996,2	MCF-7	breast:
3	chr6:109847917..109848863-chr6:110026120..110026805,4	MCF-7	breast:
4	chr6:109843965..109846639-chr6:109847963..109850929,3	K562	blood:
5	chr6:109847702..109850699-chr6:109853698..109856652,2	K562	blood:
6	chr6:109804079..109806349-chr6:109846608..109849218,2	MCF-7	breast:
7	chr6:109847880..109849128-chr6:110360138..110361223,5	K562	blood:

Variant related genes	Relation type
ENSG00000112367	Chromatin interaction
ENSG00000155085	Chromatin interaction
ENSG00000112365	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10872041	0.82[EUR][1000 genomes]
rs10872052	0.81[CEU][hapmap]
rs1096136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966009	0.81[EUR][1000 genomes]
rs11968485	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs12200787	0.93[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]
rs1925921	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]
rs1985123	0.85[EUR][1000 genomes]
rs1998812	0.84[EUR][1000 genomes]
rs2016207	0.81[CEU][hapmap]
rs2064820	0.82[EUR][1000 genomes]
rs2064822	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145144	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2357123	0.82[EUR][1000 genomes]
rs2357127	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357128	0.83[TSI][hapmap]
rs4296926	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4523125	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs4946982	0.99[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[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946997	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947004	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6568580	0.85[EUR][1000 genomes]
rs6568582	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6568583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[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[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6912368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[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	0.93[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6938741	0.91[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	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7772109	0.82[EUR][1000 genomes]
rs7773915	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7775420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829816	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs829817	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320290	0.96[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	0.93[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];0.88[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	0.93[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	0.93[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]
rs9400291	0.82[EUR][1000 genomes]
rs9400294	0.82[EUR][1000 genomes]
rs9400295	0.82[EUR][1000 genomes]
rs9400300	0.93[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	0.82[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
rs9400289	AKD1	cis	lymphoblastoid	seeQTL
rs9400289	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs9400289	SMPD2	cis	Whole Blood	GTEx
rs9400289	FIG4	cis	cerebellum	SCAN

Chromatin state (count:7 , 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
5	chr6:109847600-109848600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:109847800-109848400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr6:109847800-109848600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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