Variant report

Variant	rs2950446
Chromosome Location	chr15:42012724-42012725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10152332	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10152364	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775123	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775124	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070345	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070347	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11632100	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634840	0.87[ASN][1000 genomes]
rs11855017	0.83[ASN][1000 genomes]
rs1197768	0.86[ASN][1000 genomes]
rs1197769	0.86[ASN][1000 genomes]
rs1197772	0.86[ASN][1000 genomes]
rs12148330	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441249	0.89[ASN][1000 genomes]
rs12915325	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12916992	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1867416	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1867417	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880937	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880938	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1899820	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1899821	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1918314	0.92[ASN][1000 genomes]
rs2009310	0.81[ASN][1000 genomes]
rs2141141	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2178004	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2250964	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577947	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2577950	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2577951	0.89[ASN][1000 genomes]
rs2577953	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577954	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577955	0.95[ASN][1000 genomes]
rs2577958	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2577959	0.92[ASN][1000 genomes]
rs2605569	0.82[EUR][1000 genomes]
rs2605570	0.84[ASN][1000 genomes]
rs2695162	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695163	0.89[ASN][1000 genomes]
rs2695164	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695166	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695168	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2695169	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695170	0.84[EUR][1000 genomes]
rs2918051	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2925337	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4270151	0.82[ASN][1000 genomes]
rs4371125	0.89[ASN][1000 genomes]
rs4465584	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4923908	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924568	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924571	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924572	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62002069	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493008	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493010	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7164209	0.89[ASN][1000 genomes]
rs7169496	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169668	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177911	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178205	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027390	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028886	0.86[ASN][1000 genomes]
rs8034261	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038148	0.83[ASN][1000 genomes]
rs8038783	0.89[ASN][1000 genomes]
rs8039440	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv976925	chr15:42009106-42015264	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2950446	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr15:42002600-42015600	Weak transcription	Psoas Muscle	Psoas
10	chr15:42003600-42021800	Weak transcription	Lung	lung
11	chr15:42003600-42026800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:42003600-42027000	Weak transcription	Brain Germinal Matrix	brain
13	chr15:42003600-42028400	Weak transcription	Aorta	Aorta
14	chr15:42003800-42021400	Weak transcription	Fetal Kidney	kidney
15	chr15:42003800-42027200	Weak transcription	Spleen	Spleen
16	chr15:42003800-42028400	Weak transcription	Gastric	stomach
17	chr15:42003800-42028400	Weak transcription	Small Intestine	intestine
18	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
19	chr15:42004000-42020200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:42004000-42021200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:42004000-42021400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:42004000-42026800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:42004000-42027000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:42004200-42021400	Weak transcription	Left Ventricle	heart
25	chr15:42004600-42020200	Weak transcription	Fetal Stomach	stomach
26	chr15:42004600-42026600	Weak transcription	Right Ventricle	heart
27	chr15:42004800-42021400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:42005400-42019200	Weak transcription	HSMMtube	muscle
29	chr15:42005400-42027000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:42005400-42028400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:42005600-42018600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:42005600-42021200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:42005600-42027200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:42005600-42027400	Weak transcription	NHDF-Ad	bronchial
35	chr15:42005800-42018200	Weak transcription	K562	blood
36	chr15:42005800-42020800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:42005800-42020800	Weak transcription	HUVEC	blood vessel
38	chr15:42005800-42022600	Weak transcription	Brain Angular Gyrus	brain
39	chr15:42005800-42027000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:42005800-42028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:42006000-42019200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:42006000-42021400	Weak transcription	Brain Anterior Caudate	brain
43	chr15:42006000-42022600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:42006000-42026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr15:42006000-42028400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr15:42006200-42015400	Weak transcription	Fetal Intestine Large	intestine
47	chr15:42006200-42020600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:42006200-42021200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:42006200-42021400	Weak transcription	Brain Hippocampus Middle	brain
50	chr15:42006200-42021400	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links