Variant report

Variant	rs9320290
Chromosome Location	chr6:109838726-109838727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109837056..109838849-chr6:109842605..109844539,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10872041	0.82[EUR][1000 genomes]
rs10872052	0.80[CEU][hapmap]
rs1096136	1.00[CEU][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];0.91[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966009	0.81[EUR][1000 genomes]
rs12200787	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12524352	0.81[CEU][hapmap]
rs1358759	0.85[EUR][1000 genomes]
rs1570011	0.81[EUR][1000 genomes]
rs1570013	0.80[CEU][hapmap]
rs1590187	0.85[EUR][1000 genomes]
rs17540056	0.81[EUR][1000 genomes]
rs1925921	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[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	0.80[CEU][hapmap]
rs2064820	0.82[EUR][1000 genomes]
rs2064822	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357123	0.82[EUR][1000 genomes]
rs2357127	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296926	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4523125	0.80[CEU][hapmap]
rs4946982	0.96[AFR][1000 genomes];0.97[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]
rs4946995	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946997	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947004	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[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]
rs6568579	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6568580	0.85[EUR][1000 genomes]
rs6568582	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6568583	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568591	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568595	0.80[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	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6912368	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[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];0.83[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921303	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	0.80[CEU][hapmap]
rs6924436	0.83[EUR][1000 genomes]
rs6925886	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929823	0.81[EUR][1000 genomes]
rs6931630	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6938741	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7771729	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7772109	0.82[EUR][1000 genomes]
rs7773915	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7775420	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829817	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911022	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.90[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	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320303	1.00[CEU][hapmap]
rs9372220	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372222	0.80[CEU][hapmap]
rs9374092	0.85[EUR][1000 genomes]
rs9374095	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs9374096	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374097	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]
rs9386812	0.82[EUR][1000 genomes]
rs9386813	0.82[EUR][1000 genomes]
rs9386814	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398204	0.83[EUR][1000 genomes]
rs9400289	1.00[CEU][hapmap];0.96[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	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400312	0.80[CEU][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]
rs9487141	0.82[EUR][1000 genomes]
rs9487148	0.82[EUR][1000 genomes]
rs9487171	0.80[CEU][hapmap]
rs9487175	0.80[CEU][hapmap]
rs9487180	0.80[CEU][hapmap]
rs971432	0.80[CEU][hapmap]
rs9968792	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9320290	SMPD2	cis	Whole Blood	GTEx
rs9320290	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 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	chr6:109835600-109844400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:109837400-109839000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:109837400-109839200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:109837400-109842600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:109837600-109838800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:109837600-109838800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr6:109837600-109839000	Enhancers	Primary T cells from cord blood	blood
9	chr6:109837600-109839000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:109837800-109839000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:109837800-109839200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:109837800-109842800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:109838000-109842000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:109838400-109839000	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:109838400-109839400	Enhancers	Dnd41	blood
16	chr6:109838400-109842000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:109838400-109842200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:109838600-109839400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:109838600-109840600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:109838600-109861400	Weak transcription	Thymus	Thymus

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