Variant report

Variant	rs925104
Chromosome Location	chr15:49916655-49916656
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr15:49916157-49916731	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:49914708..49917210-chr15:49937827..49939413,2	MCF-7	breast:
2	chr15:49318492..49320476-chr15:49915801..49917383,2	K562	blood:
3	chr15:49916467..49919057-chr15:49966051..49969032,2	MCF-7	breast:

Variant related genes	Relation type
FAM227B	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10519224	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10519225	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10851478	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10851479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070695	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070699	0.82[CHB][hapmap]
rs11070706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11634947	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11637582	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11852336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853248	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854671	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855798	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs11858411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050614	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050624	0.89[ASN][1000 genomes]
rs12148716	0.92[AFR][1000 genomes]
rs12148764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12232355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591300	0.81[ASN][1000 genomes]
rs12591317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12591659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593151	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901680	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906134	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906972	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907661	0.94[ASN][1000 genomes]
rs12907918	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12907944	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908624	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912703	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916839	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1395901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395903	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17402115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs17404727	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17478694	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs17478785	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs17479589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1911612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1948975	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1976551	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2202714	0.82[CHB][hapmap]
rs2413956	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34002493	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34146550	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34246470	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34414487	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34694913	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34941109	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35698479	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4389093	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs4436732	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4480740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547278	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775816	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904469	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009977	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62021589	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62022665	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62022667	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022700	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6493372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162741	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172906	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7180421	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8032688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033476	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[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
rs925104	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49913600-49937400	Weak transcription	Spleen	Spleen
2	chr15:49914000-49917000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr15:49914000-49917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:49914000-49917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:49914000-49917800	Weak transcription	Esophagus	oesophagus
6	chr15:49914000-49917800	Weak transcription	Left Ventricle	heart
7	chr15:49914000-49917800	Weak transcription	Lung	lung
8	chr15:49914000-49930000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:49914400-49917400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:49914400-49917400	Weak transcription	Placenta	Placenta
11	chr15:49914400-49917600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:49914400-49917800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:49914400-49917800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:49914400-49917800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:49914400-49917800	Weak transcription	Aorta	Aorta
16	chr15:49914400-49917800	Weak transcription	Colonic Mucosa	Colon
17	chr15:49914400-49917800	Weak transcription	Fetal Intestine Large	intestine
18	chr15:49914400-49917800	Weak transcription	Gastric	stomach
19	chr15:49914400-49917800	Weak transcription	Right Ventricle	heart
20	chr15:49914400-49918000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:49914400-49918000	Weak transcription	Thymus	Thymus
22	chr15:49914400-49927200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:49914400-49936400	Weak transcription	Small Intestine	intestine
24	chr15:49914400-49938000	Weak transcription	Brain Substantia Nigra	brain
25	chr15:49914600-49916800	Weak transcription	Liver	Liver
26	chr15:49914600-49917000	Weak transcription	A549	lung
27	chr15:49914600-49917000	Weak transcription	HUVEC	blood vessel
28	chr15:49914600-49917400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:49914600-49917600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:49914600-49917800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:49914600-49917800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:49914600-49917800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:49914600-49917800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:49914600-49927200	Weak transcription	Fetal Brain Female	brain
35	chr15:49914600-49932600	Weak transcription	Fetal Brain Male	brain
36	chr15:49914600-49934400	Weak transcription	Stomach Mucosa	stomach
37	chr15:49914800-49916800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:49914800-49917000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:49914800-49917000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:49914800-49917400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:49914800-49917400	Weak transcription	NHEK	skin
42	chr15:49914800-49917800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:49914800-49937800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:49915000-49917200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:49915000-49917400	Weak transcription	Fetal Thymus	thymus
46	chr15:49915000-49917600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr15:49915000-49917600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:49915000-49917800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:49915000-49917800	Weak transcription	Fetal Kidney	kidney
50	chr15:49915000-49918000	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links