Variant report

Variant	rs7172906
Chromosome Location	chr15:49922775-49922776
allele	C/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:67)

rs_ID	r²[population]
rs10519224	0.85[ASN][1000 genomes]
rs10519225	0.85[ASN][1000 genomes]
rs10851479	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070695	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634947	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11637582	0.86[ASN][1000 genomes]
rs11852336	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853248	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11854671	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855798	0.85[ASN][1000 genomes]
rs11858411	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050614	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050624	0.86[ASN][1000 genomes]
rs12148716	0.85[AFR][1000 genomes]
rs12148764	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12232355	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591317	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12591659	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593151	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595692	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12901680	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902960	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906134	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12906972	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907661	0.96[ASN][1000 genomes]
rs12907918	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907944	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908624	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908635	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912703	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916839	0.85[ASN][1000 genomes]
rs1395901	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1395903	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17404727	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17478694	0.85[ASN][1000 genomes]
rs17478785	0.85[ASN][1000 genomes]
rs17479589	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1911612	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1948975	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1976551	0.96[ASN][1000 genomes]
rs2413956	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899434	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34002493	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34146550	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34246470	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34414487	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34694913	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34941109	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35698479	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4389093	0.85[ASN][1000 genomes]
rs4436732	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4480740	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4547278	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775816	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55904469	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62009977	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62021589	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022665	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022667	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62022700	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6493372	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7162741	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174135	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7180421	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8032688	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033476	0.86[ASN][1000 genomes]
rs925104	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7172906	COPS2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49913600-49937400	Weak transcription	Spleen	Spleen
2	chr15:49914000-49930000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:49914400-49927200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:49914400-49936400	Weak transcription	Small Intestine	intestine
5	chr15:49914400-49938000	Weak transcription	Brain Substantia Nigra	brain
6	chr15:49914600-49927200	Weak transcription	Fetal Brain Female	brain
7	chr15:49914600-49932600	Weak transcription	Fetal Brain Male	brain
8	chr15:49914600-49934400	Weak transcription	Stomach Mucosa	stomach
9	chr15:49914800-49937800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:49915000-49936600	Weak transcription	Pancreas	Pancrea
11	chr15:49915400-49937800	Weak transcription	Brain Anterior Caudate	brain
12	chr15:49916000-49936400	Weak transcription	Psoas Muscle	Psoas
13	chr15:49918000-49938600	Weak transcription	Right Ventricle	heart
14	chr15:49918000-49938800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:49918200-49922800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:49918200-49922800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:49918200-49922800	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:49918200-49922800	Weak transcription	Fetal Stomach	stomach
19	chr15:49918200-49923000	Weak transcription	Fetal Lung	lung
20	chr15:49918200-49923800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:49918200-49924600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:49918200-49927200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:49918200-49927200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:49918200-49927200	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:49918200-49927200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:49918200-49927200	Weak transcription	Fetal Intestine Small	intestine
27	chr15:49918200-49927200	Weak transcription	Left Ventricle	heart
28	chr15:49918200-49927400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:49918200-49927400	Weak transcription	Fetal Thymus	thymus
30	chr15:49918200-49927600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:49918200-49927600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:49918200-49927600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:49918200-49927600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:49918200-49927600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:49918200-49927600	Weak transcription	Gastric	stomach
36	chr15:49918200-49927600	Weak transcription	Lung	lung
37	chr15:49918200-49929200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:49918200-49929400	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:49918200-49929400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:49918200-49929800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr15:49918200-49931400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:49918200-49932800	Weak transcription	Thymus	Thymus
43	chr15:49918200-49933200	Weak transcription	Esophagus	oesophagus
44	chr15:49918200-49934000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:49918200-49934000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr15:49918200-49935800	Weak transcription	Brain Germinal Matrix	brain
47	chr15:49918200-49936200	Weak transcription	Aorta	Aorta
48	chr15:49918200-49936600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:49918200-49936600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:49918200-49937200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links