Variant report

Variant	rs12907944
Chromosome Location	chr15:49906971-49906972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10519224	0.87[ASN][1000 genomes]
rs10519225	0.87[ASN][1000 genomes]
rs10851478	0.86[AFR][1000 genomes]
rs10851479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070695	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634947	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11637582	0.89[ASN][1000 genomes]
rs11852336	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853248	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854671	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855798	0.87[ASN][1000 genomes]
rs11858411	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050614	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050624	0.89[ASN][1000 genomes]
rs12148716	0.92[AFR][1000 genomes]
rs12148764	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12232355	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591300	0.81[ASN][1000 genomes]
rs12591317	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12591659	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593151	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595692	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902960	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906134	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907661	0.94[ASN][1000 genomes]
rs12907918	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12908624	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916839	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1395901	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395903	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17404727	0.84[EUR][1000 genomes]
rs17478694	0.87[ASN][1000 genomes]
rs17478785	0.87[ASN][1000 genomes]
rs17479589	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1911612	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1948975	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1976551	0.94[ASN][1000 genomes]
rs2413956	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899434	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34002493	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34146550	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34246470	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34414487	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34694913	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34941109	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35698479	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4389093	0.87[ASN][1000 genomes]
rs4436732	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4480740	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547278	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904469	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009977	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62021589	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62022665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62022667	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022700	0.84[EUR][1000 genomes]
rs6493372	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162741	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172906	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174135	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7180421	0.85[EUR][1000 genomes]
rs8032688	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033476	0.89[ASN][1000 genomes]
rs925104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569392	chr15:49789413-49926300	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12907944	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49895600-49911400	Weak transcription	Psoas Muscle	Psoas
2	chr15:49895800-49907000	Weak transcription	HSMM	muscle
3	chr15:49896000-49912200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:49896600-49912000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:49896800-49907000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:49896800-49912000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:49897000-49911400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:49897200-49907000	Weak transcription	Liver	Liver
9	chr15:49897800-49907000	Weak transcription	Left Ventricle	heart
10	chr15:49897800-49911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:49898000-49907000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:49898000-49911600	Weak transcription	Brain Substantia Nigra	brain
13	chr15:49898200-49907000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:49898200-49907000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:49898200-49907000	Weak transcription	Fetal Intestine Small	intestine
16	chr15:49898200-49907000	Weak transcription	Thymus	Thymus
17	chr15:49898200-49911400	Weak transcription	Pancreas	Pancrea
18	chr15:49898200-49911800	Weak transcription	Fetal Intestine Large	intestine
19	chr15:49898200-49912200	Weak transcription	Fetal Stomach	stomach
20	chr15:49898200-49912800	Weak transcription	Esophagus	oesophagus
21	chr15:49898400-49911600	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:49898400-49912000	Weak transcription	Right Ventricle	heart
23	chr15:49899000-49907000	Weak transcription	Ovary	ovary
24	chr15:49899000-49912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:49899800-49910800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:49904600-49909400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:49905000-49912000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:49905400-49912000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:49906000-49907200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr15:49906000-49907800	ZNF genes & repeats	Primary T cells from cord blood	blood
31	chr15:49906000-49911600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:49906200-49907400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr15:49906200-49907400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
34	chr15:49906200-49907600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:49906400-49908000	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr15:49906600-49907200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr15:49906600-49907200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:49906600-49907400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:49906600-49907400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr15:49906600-49907400	ZNF genes & repeats	Fetal Lung	lung
41	chr15:49906600-49907400	ZNF genes & repeats	HSMMtube	muscle
42	chr15:49906600-49907600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr15:49906600-49908800	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr15:49906800-49907200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
45	chr15:49906800-49907200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
46	chr15:49906800-49907800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
47	chr15:49906800-49908800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:49906800-49911600	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links