Variant report

Variant	rs10872035
Chromosome Location	chr6:109837859-109837860
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: 175 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:175)

rs_ID	r²[population]
rs10457201	0.87[EUR][1000 genomes]
rs10872041	0.89[EUR][1000 genomes]
rs10872047	0.87[EUR][1000 genomes]
rs10872051	0.85[EUR][1000 genomes]
rs10872052	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1096139	0.83[EUR][1000 genomes]
rs1096140	0.82[EUR][1000 genomes]
rs1096142	0.83[EUR][1000 genomes]
rs11153193	0.85[EUR][1000 genomes]
rs11153194	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153200	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11153201	0.83[EUR][1000 genomes]
rs1115977	0.86[EUR][1000 genomes]
rs11966009	0.88[EUR][1000 genomes]
rs11968485	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12204769	0.84[EUR][1000 genomes]
rs12211805	0.81[EUR][1000 genomes]
rs12215867	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12524352	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12663674	0.83[EUR][1000 genomes]
rs1321327	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1358759	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1406957	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1474959	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1570011	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1570012	0.87[EUR][1000 genomes]
rs1570013	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1575108	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1575109	0.85[EUR][1000 genomes]
rs1590187	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1885425	0.82[EUR][1000 genomes]
rs1967725	0.86[EUR][1000 genomes]
rs1969710	0.85[EUR][1000 genomes]
rs1969711	0.86[EUR][1000 genomes]
rs1985123	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1998812	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016207	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2064820	0.89[EUR][1000 genomes]
rs2093097	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2145144	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2208210	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2357123	0.89[EUR][1000 genomes]
rs2357125	0.87[EUR][1000 genomes]
rs2357128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2357129	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2357130	0.85[EUR][1000 genomes]
rs2884101	0.85[EUR][1000 genomes]
rs4454170	0.85[EUR][1000 genomes]
rs4523125	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4591898	0.82[EUR][1000 genomes]
rs4607459	0.83[EUR][1000 genomes]
rs4945835	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4946986	0.89[EUR][1000 genomes]
rs4946987	0.89[EUR][1000 genomes]
rs4946989	0.87[EUR][1000 genomes]
rs4946991	0.84[EUR][1000 genomes]
rs4946992	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4946993	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946996	0.84[EUR][1000 genomes]
rs4946999	0.85[EUR][1000 genomes]
rs4947003	0.84[EUR][1000 genomes]
rs62435981	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6568580	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6568590	0.84[EUR][1000 genomes]
rs6568594	0.82[EUR][1000 genomes]
rs6568595	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6568596	0.82[EUR][1000 genomes]
rs6568600	0.80[EUR][1000 genomes]
rs67715693	0.86[EUR][1000 genomes]
rs6911838	0.82[YRI][hapmap]
rs6916239	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6917999	0.82[EUR][1000 genomes]
rs6918140	0.82[EUR][1000 genomes]
rs6922784	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6924269	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6929823	0.88[EUR][1000 genomes]
rs6938499	0.83[EUR][1000 genomes]
rs731879	0.84[EUR][1000 genomes]
rs7450970	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7453835	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7454678	0.85[EUR][1000 genomes]
rs7454858	0.81[EUR][1000 genomes]
rs7744981	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7745469	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7749386	0.86[EUR][1000 genomes]
rs7749910	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7751458	0.81[EUR][1000 genomes]
rs7754118	0.86[EUR][1000 genomes]
rs7754606	0.86[EUR][1000 genomes]
rs7761008	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7764783	0.84[EUR][1000 genomes]
rs7765265	0.85[EUR][1000 genomes]
rs829813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829815	0.84[EUR][1000 genomes]
rs829816	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs829818	0.84[EUR][1000 genomes]
rs853544	0.82[EUR][1000 genomes]
rs9320294	0.87[EUR][1000 genomes]
rs9320295	0.88[EUR][1000 genomes]
rs9320296	0.88[EUR][1000 genomes]
rs9320299	0.88[EUR][1000 genomes]
rs9320304	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9320305	0.86[EUR][1000 genomes]
rs9372216	0.86[EUR][1000 genomes]
rs9372221	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9372222	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9374092	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9374094	0.82[EUR][1000 genomes]
rs9374095	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9374097	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9374098	0.87[EUR][1000 genomes]
rs9374099	0.89[EUR][1000 genomes]
rs9374108	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9374110	0.96[CEU][hapmap]
rs9374113	0.84[EUR][1000 genomes]
rs9374114	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9384713	0.89[EUR][1000 genomes]
rs9384715	0.88[EUR][1000 genomes]
rs9384716	0.87[EUR][1000 genomes]
rs9384717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9384720	0.84[EUR][1000 genomes]
rs9386812	0.89[EUR][1000 genomes]
rs9386813	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9386816	0.86[EUR][1000 genomes]
rs9386818	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9386823	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9386824	0.96[CEU][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs9386825	0.86[EUR][1000 genomes]
rs9386826	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs9398204	0.90[EUR][1000 genomes]
rs9398206	0.87[EUR][1000 genomes]
rs9400288	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9400291	0.89[EUR][1000 genomes]
rs9400293	0.83[EUR][1000 genomes]
rs9400294	0.89[EUR][1000 genomes]
rs9400295	0.89[EUR][1000 genomes]
rs9400301	0.86[EUR][1000 genomes]
rs9400307	0.82[EUR][1000 genomes]
rs9400310	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9400312	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9400313	0.96[CEU][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs9400314	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9400315	0.84[EUR][1000 genomes]
rs9400316	0.96[CEU][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs942923	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs942924	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9480973	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9480974	0.89[EUR][1000 genomes]
rs9480976	0.89[EUR][1000 genomes]
rs9480982	0.86[EUR][1000 genomes]
rs9480984	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9480985	0.84[EUR][1000 genomes]
rs9480986	0.84[EUR][1000 genomes]
rs9480991	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9487141	0.89[EUR][1000 genomes]
rs9487148	0.89[EUR][1000 genomes]
rs9487152	0.84[EUR][1000 genomes]
rs9487153	0.83[EUR][1000 genomes]
rs9487156	0.87[EUR][1000 genomes]
rs9487160	0.86[EUR][1000 genomes]
rs9487164	0.85[EUR][1000 genomes]
rs9487170	0.86[EUR][1000 genomes]
rs9487171	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9487172	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9487175	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9487176	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9487178	0.84[EUR][1000 genomes]
rs9487179	0.80[EUR][1000 genomes]
rs9487180	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9487183	0.82[EUR][1000 genomes]
rs971432	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs971433	0.84[EUR][1000 genomes]
rs9986423	0.84[EUR][1000 genomes]
rs9986507	0.96[CEU][hapmap];0.86[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10872035	SMPD2	cis	Whole Blood	GTEx
rs10872035	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 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	chr6:109836600-109838600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:109836600-109838600	Enhancers	Thymus	Thymus
5	chr6:109836800-109838000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:109836800-109838000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr6:109837000-109838000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr6:109837000-109838400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr6:109837400-109838400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:109837400-109838400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:109837400-109838600	Enhancers	Fetal Thymus	thymus
12	chr6:109837400-109839000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:109837400-109839200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:109837400-109842600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:109837600-109838200	Weak transcription	Primary B cells from cord blood	blood
16	chr6:109837600-109838200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:109837600-109838400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr6:109837600-109838600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:109837600-109838600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:109837600-109838600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:109837600-109838800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:109837600-109838800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:109837600-109839000	Enhancers	Primary T cells from cord blood	blood
24	chr6:109837600-109839000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:109837800-109838400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:109837800-109838400	Flanking Active TSS	Dnd41	blood
27	chr6:109837800-109838600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr6:109837800-109839000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:109837800-109839200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:109837800-109842800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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