Variant report

Variant	rs11854039
Chromosome Location	chr15:49496472-49496473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10519224	1.00[AFR][1000 genomes]
rs10519225	1.00[AFR][1000 genomes]
rs11853969	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11854557	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11855798	1.00[AFR][1000 genomes]
rs11857515	0.88[AFR][1000 genomes]
rs11857773	0.83[ASN][1000 genomes]
rs11858814	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591300	0.96[AFR][1000 genomes]
rs12899422	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900838	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12901353	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901929	1.00[AFR][1000 genomes]
rs12902096	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12902271	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12905094	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12905477	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12914876	0.88[AFR][1000 genomes]
rs12916839	0.88[AFR][1000 genomes]
rs17393761	0.81[ASN][1000 genomes]
rs17435932	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17472989	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17478694	0.92[AFR][1000 genomes]
rs17478785	0.92[AFR][1000 genomes]
rs1961393	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289389	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34562714	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748066	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023246	1.00[AFR][1000 genomes]
rs36100631	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774538	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4775806	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs55979115	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62009762	0.85[ASN][1000 genomes]
rs62009834	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71467664	0.81[ASN][1000 genomes]
rs7180168	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7497335	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8029687	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033184	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8043493	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672848	0.81[AFR][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	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11854039	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463200-49508200	Weak transcription	Ovary	ovary
2	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:49463600-49527800	Weak transcription	HSMM	muscle
4	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
5	chr15:49464400-49500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:49465400-49508200	Weak transcription	Hela-S3	cervix
7	chr15:49472800-49497200	Weak transcription	Brain Anterior Caudate	brain
8	chr15:49478400-49497400	Weak transcription	Primary B cells from cord blood	blood
9	chr15:49480000-49510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:49480200-49500200	Weak transcription	Spleen	Spleen
11	chr15:49480200-49502000	Weak transcription	Aorta	Aorta
12	chr15:49480200-49503800	Weak transcription	Esophagus	oesophagus
13	chr15:49480600-49503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:49481600-49498600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:49483600-49497000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:49484200-49519400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:49484400-49497000	Weak transcription	Fetal Brain Male	brain
18	chr15:49487000-49510600	Weak transcription	Thymus	Thymus
19	chr15:49487200-49531200	Weak transcription	HMEC	breast
20	chr15:49489200-49508000	Weak transcription	Gastric	stomach
21	chr15:49489400-49496800	Weak transcription	HepG2	liver
22	chr15:49489400-49508200	Weak transcription	Pancreas	Pancrea
23	chr15:49489800-49499000	Weak transcription	Dnd41	blood
24	chr15:49490000-49499400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:49490800-49508400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:49491400-49498000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:49491400-49510600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:49491600-49496600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:49491800-49496800	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:49492000-49497400	Weak transcription	Brain Angular Gyrus	brain
31	chr15:49492000-49517600	Weak transcription	NHLF	lung
32	chr15:49492000-49520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:49492000-49527800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:49492000-49530200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
36	chr15:49492200-49497600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:49492200-49499600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:49492200-49499600	Weak transcription	Fetal Lung	lung
39	chr15:49492200-49512800	Weak transcription	NHDF-Ad	bronchial
40	chr15:49492600-49503800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:49492800-49497200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:49492800-49498000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:49492800-49514600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:49493000-49497600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:49493000-49503800	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:49493000-49520000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:49493400-49496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:49493400-49496600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:49493400-49496600	Weak transcription	Fetal Brain Female	brain
50	chr15:49493800-49496600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links