Variant report

Variant	rs1466276
Chromosome Location	chr15:52025950-52025951
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51997906..52000590-chr15:52024148..52026004,2	MCF-7	breast:
2	chr15:52017571..52019095-chr15:52024523..52026773,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10444798	0.81[AMR][1000 genomes]
rs10444823	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs10775145	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs11070864	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133882	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11630084	0.89[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11632106	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636345	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11638766	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11638820	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12903707	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs12905283	0.84[AMR][1000 genomes]
rs12917133	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1350174	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545602	0.89[CEU][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1811326	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs1867984	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs1902430	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1972689	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2014638	0.92[CEU][hapmap]
rs2034857	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2034858	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2077743	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168475	0.84[ASN][1000 genomes]
rs2264339	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2303443	0.92[CEU][hapmap]
rs2414116	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2414117	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414119	0.81[AMR][1000 genomes]
rs2554305	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs2554307	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2554308	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2554332	0.89[CEU][hapmap]
rs2554336	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2554349	0.87[CHB][hapmap]
rs2570224	0.92[CEU][hapmap]
rs2570228	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2570233	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2570252	0.89[CEU][hapmap]
rs2570253	0.89[CEU][hapmap]
rs2570258	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2593173	0.82[CHB][hapmap]
rs2623251	0.81[CEU][hapmap]
rs2623254	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs2623259	0.92[CEU][hapmap]
rs2623263	0.81[CEU][hapmap]
rs2623281	0.82[CHB][hapmap]
rs2623283	0.83[CHB][hapmap]
rs3751596	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs3794530	0.81[AMR][1000 genomes]
rs3794534	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs3794535	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs3794536	0.84[AMR][1000 genomes]
rs4238383	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4502160	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4534783	0.81[AMR][1000 genomes]
rs4622456	0.89[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774602	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4775978	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4775982	0.89[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes]
rs4775983	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs526556	0.83[ASN][1000 genomes]
rs6493515	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6493518	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493519	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493523	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs689884	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7163176	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165283	0.89[CEU][hapmap]
rs7165585	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166110	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7171459	0.84[AMR][1000 genomes]
rs7173375	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7181553	0.92[CEU][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8024081	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8024088	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8024589	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8026521	0.84[AMR][1000 genomes]
rs8028258	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028890	0.89[CEU][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8041268	0.84[AMR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1466276	LYSMD2	cis	Muscle Skeletal	GTEx
rs1466276	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52013600-52028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:52013600-52028400	Weak transcription	Fetal Brain Female	brain
3	chr15:52013600-52028800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:52019000-52028200	Weak transcription	Brain Substantia Nigra	brain
5	chr15:52020000-52028800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:52020200-52028000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:52020200-52029000	Weak transcription	NH-A	brain
8	chr15:52020400-52028000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:52022400-52026000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:52023600-52028200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:52024200-52026200	Enhancers	Psoas Muscle	Psoas
12	chr15:52024200-52028000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:52024200-52028000	Weak transcription	Hela-S3	cervix
14	chr15:52024200-52028400	Flanking Active TSS	GM12878-XiMat	blood
15	chr15:52024400-52026400	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:52024400-52026800	Enhancers	Spleen	Spleen
17	chr15:52024400-52027800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr15:52024400-52027800	Enhancers	Brain Anterior Caudate	brain
19	chr15:52024400-52028000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:52024400-52028400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:52024400-52028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:52024400-52028400	Enhancers	Fetal Thymus	thymus
23	chr15:52024400-52028400	Enhancers	Thymus	Thymus
24	chr15:52024400-52028800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:52024400-52028800	Weak transcription	Right Ventricle	heart
26	chr15:52024600-52026400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:52024600-52026800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr15:52024600-52026800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr15:52024600-52027600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:52024600-52027600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:52024600-52027600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:52024600-52027600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:52024600-52027800	Enhancers	Primary hematopoietic stem cells	blood
34	chr15:52024600-52027800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:52024600-52027800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr15:52024600-52028000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr15:52024600-52028000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr15:52024600-52028200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr15:52024600-52028200	Weak transcription	NHDF-Ad	bronchial
40	chr15:52024600-52028200	Weak transcription	NHLF	lung
41	chr15:52024600-52028400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:52024600-52028400	Weak transcription	Aorta	Aorta
43	chr15:52024600-52028400	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:52024600-52028400	Weak transcription	Gastric	stomach
45	chr15:52024600-52028400	Weak transcription	NHEK	skin
46	chr15:52024600-52028600	Weak transcription	Fetal Stomach	stomach
47	chr15:52024600-52028800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:52024600-52028800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:52024600-52028800	Weak transcription	Osteobl	bone
50	chr15:52024600-52029000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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