Variant report

Variant	rs12441249
Chromosome Location	chr15:41984538-41984539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10152332	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152364	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775124	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070345	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070347	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]
rs11070350	0.81[EUR][1000 genomes]
rs11632100	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634840	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639146	0.84[ASN][1000 genomes]
rs11639249	0.84[ASN][1000 genomes]
rs11855017	0.81[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197670	0.81[EUR][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs1197768	0.90[ASN][1000 genomes]
rs1197769	0.90[ASN][1000 genomes]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12148330	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]
rs12900295	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.82[ASN][1000 genomes]
rs12915325	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]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648827	0.81[EUR][1000 genomes]
rs1648828	0.81[EUR][1000 genomes]
rs1648829	0.80[EUR][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs1648831	0.81[EUR][1000 genomes]
rs1648832	0.81[EUR][1000 genomes]
rs1648833	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1648834	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1648835	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1672464	0.81[EUR][1000 genomes]
rs1672465	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1672466	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16972089	0.93[CEU][hapmap]
rs16972136	1.00[CEU][hapmap]
rs1867416	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867417	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]
rs1880937	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009310	0.91[ASN][1000 genomes]
rs2141141	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178004	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]
rs2250964	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577952	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2577953	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605570	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2695162	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695166	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695168	0.92[ASN][1000 genomes]
rs2695169	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2918051	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2950446	0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270151	0.92[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924571	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57498313	0.81[EUR][1000 genomes]
rs62002069	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6493008	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493010	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164209	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165230	0.81[EUR][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169668	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176474	0.89[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027390	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028886	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030179	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890508	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12441249	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
2	chr15:41955000-41988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:41959400-41988600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:41959400-41989000	Weak transcription	NHDF-Ad	bronchial
5	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:41962000-41988400	Weak transcription	Adipose Nuclei	Adipose
7	chr15:41962000-41990800	Weak transcription	NH-A	brain
8	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:41962000-42001400	Weak transcription	Gastric	stomach
10	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:41962600-41988400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:41963400-41988400	Weak transcription	Placenta	Placenta
13	chr15:41963600-41987800	Weak transcription	Primary B cells from cord blood	blood
14	chr15:41966600-41988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:41968800-41988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:41971600-41988200	Weak transcription	Fetal Thymus	thymus
17	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:41972000-41989600	Weak transcription	Fetal Intestine Small	intestine
19	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
21	chr15:41973200-41988400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:41975800-41988400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:41976000-41988000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:41976800-41988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:41978400-41985000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr15:41978800-41985000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr15:41978800-41991200	Weak transcription	Liver	Liver
28	chr15:41980000-41984800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:41980600-41984600	Enhancers	Dnd41	blood
30	chr15:41980600-41984800	Enhancers	K562	blood
31	chr15:41980600-41985000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr15:41980600-41987400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr15:41980600-41988200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:41980800-41988400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:41981000-41984800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:41981000-41988400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:41981200-41988400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:41981600-41988400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:41981600-41988400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:41981600-41995800	Weak transcription	Fetal Stomach	stomach
41	chr15:41981800-41984800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr15:41982000-41984800	Enhancers	HepG2	liver
43	chr15:41982200-41984600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr15:41982200-41985000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr15:41982400-41984600	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr15:41982400-41988200	Weak transcription	Brain Substantia Nigra	brain
47	chr15:41982600-41984600	Enhancers	Primary T cells from cord blood	blood
48	chr15:41982600-41984600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr15:41983000-41984600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr15:41983000-42001200	Weak transcription	Ovary	ovary

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