Variant report

Variant	rs2178004
Chromosome Location	chr15:41991315-41991316
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.81[EUR][1000 genomes]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775124	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap]
rs11070345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632100	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634840	0.82[AMR][1000 genomes];0.84[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	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs1197768	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197769	0.86[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];1.00[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900295	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.89[AMR][1000 genomes];0.84[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916525	0.93[AMR][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[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];0.81[EUR][1000 genomes]
rs16972136	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1867416	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867417	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]
rs1880937	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.84[AMR][1000 genomes];0.98[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];0.85[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009310	0.91[ASN][1000 genomes]
rs2141141	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250964	0.95[AMR][1000 genomes];0.98[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];0.96[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];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577953	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605569	0.90[EUR][1000 genomes]
rs2605570	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695162	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[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];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695166	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695168	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695169	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695170	0.92[EUR][1000 genomes]
rs2918051	0.84[AMR][1000 genomes];0.98[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];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2950446	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270151	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.84[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];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924571	1.00[AMR][1000 genomes];0.98[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002067	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62002069	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493010	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164209	0.85[AMR][1000 genomes];0.82[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169668	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176474	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177232	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027390	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028886	0.82[AMR][1000 genomes];0.84[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];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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];0.84[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];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2178004	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
2	chr15:41962000-42001400	Weak transcription	Gastric	stomach
3	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
7	chr15:41981600-41995800	Weak transcription	Fetal Stomach	stomach
8	chr15:41983000-42001200	Weak transcription	Ovary	ovary
9	chr15:41983200-42002600	Weak transcription	Small Intestine	intestine
10	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:41984400-42002800	Weak transcription	A549	lung
12	chr15:41984600-41993000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:41984600-41999200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:41984600-41999400	Weak transcription	Thymus	Thymus
15	chr15:41984600-41999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:41984600-42000600	Weak transcription	Lung	lung
17	chr15:41984600-42001600	Weak transcription	Pancreas	Pancrea
18	chr15:41984800-41991800	Weak transcription	Spleen	Spleen
19	chr15:41984800-41998800	Weak transcription	Left Ventricle	heart
20	chr15:41984800-41999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:41984800-42000800	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:41984800-42001200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:41984800-42001400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:41984800-42003000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:41985200-41996000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:41987600-42001200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:41988200-41991400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:41988200-41995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:41988600-42001200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:41988600-42003000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:41988600-42003000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:41988800-41994600	Strong transcription	Fetal Thymus	thymus
33	chr15:41988800-42002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr15:41988800-42003000	Weak transcription	Fetal Kidney	kidney
35	chr15:41989000-41992400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:41989000-41993600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:41989000-41997400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:41989000-41999000	Weak transcription	Fetal Lung	lung
39	chr15:41989000-42003000	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
41	chr15:41989200-41991600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:41989200-41992600	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:41989200-41993200	Weak transcription	GM12878-XiMat	blood
44	chr15:41989200-41993600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:41989200-41993600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:41989200-41993800	Strong transcription	Primary T cells from cord blood	blood
47	chr15:41989200-41998800	Weak transcription	Dnd41	blood
48	chr15:41989200-41999400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:41989200-41999400	Weak transcription	Placenta	Placenta
50	chr15:41989200-42000400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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