Variant report

Variant	rs1867417
Chromosome Location	chr15:41964134-41964135
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	chr15:41954547..41956323-chr15:41964116..41966547,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10152332	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775124	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap]
rs11070345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632100	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634840	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639146	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11639249	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11855017	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197704	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1197768	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197769	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900295	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916525	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1648833	1.00[CEU][hapmap]
rs1648834	1.00[CEU][hapmap]
rs1648835	1.00[CEU][hapmap]
rs1672465	1.00[CEU][hapmap]
rs1672466	1.00[CEU][hapmap]
rs16972089	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs16972136	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1867416	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880937	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009310	0.91[ASN][1000 genomes]
rs2141141	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250964	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577953	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605569	0.88[EUR][1000 genomes]
rs2605570	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695162	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695166	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695168	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695169	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695170	0.91[EUR][1000 genomes]
rs2918051	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2950446	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270151	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002067	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62002069	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493010	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164209	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169668	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176474	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177232	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027390	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028886	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030179	0.89[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038148	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1867417	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954400-41964600	Weak transcription	Lung	lung
2	chr15:41954400-41970600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:41954400-41978600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:41954400-41982800	Weak transcription	Small Intestine	intestine
5	chr15:41954600-41964200	Weak transcription	Fetal Stomach	stomach
6	chr15:41954600-41964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:41954600-41965600	Weak transcription	Left Ventricle	heart
8	chr15:41954600-41976200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:41954600-41983800	Weak transcription	Thymus	Thymus
10	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
11	chr15:41954800-41964400	Weak transcription	Brain Angular Gyrus	brain
12	chr15:41954800-41964400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:41954800-41964400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:41954800-41964600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:41954800-41969000	Weak transcription	Fetal Brain Female	brain
16	chr15:41954800-41976200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:41954800-41980800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:41955000-41964400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:41955000-41972600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:41955000-41988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:41955200-41964200	Weak transcription	Brain Anterior Caudate	brain
22	chr15:41955200-41968200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:41955400-41964800	Weak transcription	Fetal Brain Male	brain
24	chr15:41955400-41965800	Weak transcription	Fetal Intestine Small	intestine
25	chr15:41958400-41978400	Weak transcription	Pancreas	Pancrea
26	chr15:41958800-41973400	Weak transcription	HMEC	breast
27	chr15:41959000-41964200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:41959000-41965000	Weak transcription	Fetal Kidney	kidney
29	chr15:41959200-41964200	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:41959400-41988600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:41959400-41989000	Weak transcription	NHDF-Ad	bronchial
32	chr15:41959600-41981000	Weak transcription	Osteobl	bone
33	chr15:41961400-41967200	Weak transcription	Dnd41	blood
34	chr15:41961600-41975400	Weak transcription	Aorta	Aorta
35	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:41962000-41968400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:41962000-41969800	Weak transcription	NHEK	skin
38	chr15:41962000-41980200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:41962000-41983800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:41962000-41988400	Weak transcription	Adipose Nuclei	Adipose
41	chr15:41962000-41990800	Weak transcription	NH-A	brain
42	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:41962000-42001400	Weak transcription	Gastric	stomach
44	chr15:41962200-41964200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:41962200-41964400	Weak transcription	Psoas Muscle	Psoas
46	chr15:41962200-41964600	Weak transcription	Brain Germinal Matrix	brain
47	chr15:41962200-41965800	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:41962200-41966000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:41962200-41966200	Weak transcription	Liver	Liver
50	chr15:41962200-41967000	Weak transcription	Rectal Mucosa Donor 31	rectum

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