Variant report

Variant	rs12916992
Chromosome Location	chr15:41975127-41975128
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	chr15:41973132..41976112-chr15:41981516..41983125,2	K562	blood:
2	chr15:41952625..41954330-chr15:41973061..41975209,2	K562	blood:

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];0.81[CHB][hapmap]
rs10152332	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152364	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775124	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap]
rs11070345	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070347	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]
rs11632100	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634840	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639146	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11639249	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11855017	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197704	0.90[CHB][hapmap]
rs1197768	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197769	0.85[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441249	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]
rs12900295	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12915325	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]
rs12916525	0.91[AMR][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.81[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	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs16972136	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1867416	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867417	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]
rs1880937	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[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	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178004	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]
rs2250964	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	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]
rs2577950	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]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577953	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.82[AMR][1000 genomes];0.95[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	0.89[EUR][1000 genomes]
rs2605570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695162	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695164	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]
rs2695166	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695168	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695169	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695170	0.91[EUR][1000 genomes]
rs2918051	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2950446	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270151	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4371125	0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924571	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002067	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62002069	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493008	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493010	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164209	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169668	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176474	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177232	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027390	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028886	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030179	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[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];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[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
rs12916992	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954400-41978600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:41954400-41982800	Weak transcription	Small Intestine	intestine
3	chr15:41954600-41976200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:41954600-41983800	Weak transcription	Thymus	Thymus
5	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
6	chr15:41954800-41976200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:41954800-41980800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:41955000-41988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:41958400-41978400	Weak transcription	Pancreas	Pancrea
10	chr15:41959400-41988600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:41959400-41989000	Weak transcription	NHDF-Ad	bronchial
12	chr15:41959600-41981000	Weak transcription	Osteobl	bone
13	chr15:41961600-41975400	Weak transcription	Aorta	Aorta
14	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:41962000-41980200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:41962000-41983800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:41962000-41988400	Weak transcription	Adipose Nuclei	Adipose
18	chr15:41962000-41990800	Weak transcription	NH-A	brain
19	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:41962000-42001400	Weak transcription	Gastric	stomach
21	chr15:41962200-41984400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:41962600-41981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:41962600-41981800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:41962600-41983400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:41962600-41983600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:41962600-41984000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:41962600-41988400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:41963400-41988400	Weak transcription	Placenta	Placenta
30	chr15:41963600-41987800	Weak transcription	Primary B cells from cord blood	blood
31	chr15:41964400-41975800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:41964600-41981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:41964600-41982200	Weak transcription	Ovary	ovary
34	chr15:41964800-41983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:41965000-41980600	Weak transcription	K562	blood
36	chr15:41965000-41982400	Weak transcription	Brain Anterior Caudate	brain
37	chr15:41966600-41984400	Weak transcription	Left Ventricle	heart
38	chr15:41966600-41988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:41967600-41976400	Weak transcription	A549	lung
40	chr15:41967600-41976400	Weak transcription	HepG2	liver
41	chr15:41967600-41982600	Weak transcription	GM12878-XiMat	blood
42	chr15:41967800-41980600	Weak transcription	Dnd41	blood
43	chr15:41968400-41975400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:41968400-41982200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:41968800-41988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:41970600-41976600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:41971200-41980600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:41971200-41980800	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:41971400-41976800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr15:41971600-41980400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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