Variant report

Variant	rs7162741
Chromosome Location	chr15:49905410-49905411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49904832..49906457-chr15:49910761..49913001,2	MCF-7	breast:
2	chr15:49902751..49906508-chr15:49911553..49916150,4	K562	blood:
3	chr15:49901830..49905656-chr15:49909277..49913053,4	K562	blood:

Variant related genes	Relation type
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10519224	0.86[ASN][1000 genomes]
rs10519225	0.86[ASN][1000 genomes]
rs10851479	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070695	0.89[ASN][1000 genomes]
rs11637582	0.87[ASN][1000 genomes]
rs11852336	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11853248	0.95[ASN][1000 genomes]
rs11854671	0.94[ASN][1000 genomes]
rs11855798	0.86[ASN][1000 genomes]
rs11858411	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12050614	0.99[ASN][1000 genomes]
rs12050624	0.87[ASN][1000 genomes]
rs12148716	0.85[AFR][1000 genomes]
rs12148764	0.96[ASN][1000 genomes]
rs12232355	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591317	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591659	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12593151	0.96[ASN][1000 genomes]
rs12595692	0.96[ASN][1000 genomes]
rs12901680	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902960	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906134	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12906972	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12907661	0.92[ASN][1000 genomes]
rs12907918	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12907944	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12908624	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12908635	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912703	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916839	0.86[ASN][1000 genomes]
rs1395901	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1395903	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17478694	0.86[ASN][1000 genomes]
rs17478785	0.86[ASN][1000 genomes]
rs17479589	0.96[ASN][1000 genomes]
rs1911612	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1948975	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1976551	0.92[ASN][1000 genomes]
rs2413956	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2899434	0.96[ASN][1000 genomes]
rs34002493	0.96[ASN][1000 genomes]
rs34146550	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34246470	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34414487	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34694913	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34941109	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35698479	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4389093	0.86[ASN][1000 genomes]
rs4436732	0.96[ASN][1000 genomes]
rs4480740	0.96[ASN][1000 genomes]
rs4547278	0.96[ASN][1000 genomes]
rs4775816	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55904469	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62009977	0.96[ASN][1000 genomes]
rs62021589	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62022665	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62022667	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6493372	0.96[ASN][1000 genomes]
rs7172906	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174135	0.96[ASN][1000 genomes]
rs8032688	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8033476	0.87[ASN][1000 genomes]
rs925104	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[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
rs7162741	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49893200-49906800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:49895600-49911400	Weak transcription	Psoas Muscle	Psoas
3	chr15:49895800-49907000	Weak transcription	HSMM	muscle
4	chr15:49896000-49912200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:49896200-49906600	Weak transcription	Fetal Lung	lung
6	chr15:49896600-49906200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr15:49896600-49912000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:49896800-49907000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:49896800-49912000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:49897000-49911400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:49897200-49907000	Weak transcription	Liver	Liver
12	chr15:49897600-49906200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:49897600-49906400	Weak transcription	Primary B cells from cord blood	blood
14	chr15:49897800-49906800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:49897800-49907000	Weak transcription	Left Ventricle	heart
16	chr15:49897800-49911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:49898000-49906600	Weak transcription	HSMMtube	muscle
18	chr15:49898000-49907000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:49898000-49911600	Weak transcription	Brain Substantia Nigra	brain
20	chr15:49898200-49906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:49898200-49906600	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:49898200-49907000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:49898200-49907000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:49898200-49907000	Weak transcription	Fetal Intestine Small	intestine
25	chr15:49898200-49907000	Weak transcription	Thymus	Thymus
26	chr15:49898200-49911400	Weak transcription	Pancreas	Pancrea
27	chr15:49898200-49911800	Weak transcription	Fetal Intestine Large	intestine
28	chr15:49898200-49912200	Weak transcription	Fetal Stomach	stomach
29	chr15:49898200-49912800	Weak transcription	Esophagus	oesophagus
30	chr15:49898400-49906800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:49898400-49911600	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:49898400-49912000	Weak transcription	Right Ventricle	heart
33	chr15:49898600-49906000	Weak transcription	Primary T cells from cord blood	blood
34	chr15:49899000-49907000	Weak transcription	Ovary	ovary
35	chr15:49899000-49912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:49899600-49906600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:49899800-49910800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:49904000-49906600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:49904600-49906000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:49904600-49909400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:49905000-49912000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:49905200-49905600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr15:49905200-49905800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:49905200-49906000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:49905400-49905800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
46	chr15:49905400-49912000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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