Variant report

Variant	rs2250964
Chromosome Location	chr15:42017542-42017543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10152332	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152364	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775122	0.86[AMR][1000 genomes]
rs10775123	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775124	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070345	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070347	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632100	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634840	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11639146	0.83[AMR][1000 genomes]
rs11855017	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197670	0.81[ASN][1000 genomes]
rs1197768	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197769	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197772	0.90[ASN][1000 genomes]
rs12148330	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441249	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900295	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12902548	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12915325	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916525	0.88[AMR][1000 genomes]
rs12916992	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16972089	0.83[EUR][1000 genomes]
rs16972136	0.81[EUR][1000 genomes]
rs1867416	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867417	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880937	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1899819	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1899820	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1899821	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1918314	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009310	0.85[ASN][1000 genomes]
rs2141141	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178004	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577950	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577951	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577952	0.81[ASN][1000 genomes]
rs2577953	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577954	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577955	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577958	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577959	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2605569	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605570	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695162	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695164	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695166	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695168	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695169	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695170	0.94[EUR][1000 genomes]
rs2918051	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925337	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950446	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244585	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4270151	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4371125	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4465584	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923908	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924568	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924571	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924572	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62002067	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62002069	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493008	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493010	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164209	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169496	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169668	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176474	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7177232	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7177911	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178205	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8027390	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028886	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030179	0.83[ASN][1000 genomes]
rs8034261	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038148	0.87[ASN][1000 genomes]
rs8038783	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039440	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
4	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1041861	chr15:42016097-42062287	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv988006	chr15:42016301-42026157	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3525217	chr15:42016843-42018640	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3331143	chr15:42017010-42019008	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv6726	chr15:42017449-42018334	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2250964	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
4	chr15:41995400-42023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41996200-42034800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:41999800-42018400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:42002000-42021400	Weak transcription	Esophagus	oesophagus
8	chr15:42002200-42028400	Weak transcription	Pancreas	Pancrea
9	chr15:42003600-42021800	Weak transcription	Lung	lung
10	chr15:42003600-42026800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:42003600-42027000	Weak transcription	Brain Germinal Matrix	brain
12	chr15:42003600-42028400	Weak transcription	Aorta	Aorta
13	chr15:42003800-42021400	Weak transcription	Fetal Kidney	kidney
14	chr15:42003800-42027200	Weak transcription	Spleen	Spleen
15	chr15:42003800-42028400	Weak transcription	Gastric	stomach
16	chr15:42003800-42028400	Weak transcription	Small Intestine	intestine
17	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
18	chr15:42004000-42020200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:42004000-42021200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:42004000-42021400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:42004000-42026800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:42004000-42027000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:42004200-42021400	Weak transcription	Left Ventricle	heart
24	chr15:42004600-42020200	Weak transcription	Fetal Stomach	stomach
25	chr15:42004600-42026600	Weak transcription	Right Ventricle	heart
26	chr15:42004800-42021400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:42005400-42019200	Weak transcription	HSMMtube	muscle
28	chr15:42005400-42027000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:42005400-42028400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:42005600-42018600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:42005600-42021200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:42005600-42027200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:42005600-42027400	Weak transcription	NHDF-Ad	bronchial
34	chr15:42005800-42018200	Weak transcription	K562	blood
35	chr15:42005800-42020800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:42005800-42020800	Weak transcription	HUVEC	blood vessel
37	chr15:42005800-42022600	Weak transcription	Brain Angular Gyrus	brain
38	chr15:42005800-42027000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:42005800-42028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:42006000-42019200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:42006000-42021400	Weak transcription	Brain Anterior Caudate	brain
42	chr15:42006000-42022600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:42006000-42026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:42006000-42028400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:42006200-42020600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:42006200-42021200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:42006200-42021400	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:42006200-42021400	Weak transcription	Ovary	ovary
49	chr15:42006200-42021400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:42006200-42022600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links