Variant report

Variant	rs10783289
Chromosome Location	chr12:49299195-49299196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49258556..49260730-chr12:49298046..49299547,2	MCF-7	breast:
2	chr12:49299067..49301017-chr12:49305667..49307889,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172602	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1051886	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1054376	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10747556	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10747557	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10747558	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs10783290	0.94[ASN][1000 genomes]
rs10783292	0.90[ASN][1000 genomes]
rs10783293	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10783294	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10783295	0.95[ASN][1000 genomes]
rs10783297	0.90[ASN][1000 genomes]
rs10875883	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs10875885	0.82[CHB][hapmap]
rs10875886	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10875888	0.85[ASN][1000 genomes]
rs10875893	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs10875894	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875895	0.95[ASN][1000 genomes]
rs10875896	0.89[ASN][1000 genomes]
rs10875897	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875898	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875900	0.89[ASN][1000 genomes]
rs10875901	0.88[ASN][1000 genomes]
rs10875902	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1111662	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168773	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11168779	0.97[ASN][1000 genomes]
rs11168783	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11168784	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11168785	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11168790	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11168792	0.94[ASN][1000 genomes]
rs11168794	0.94[ASN][1000 genomes]
rs11168795	0.89[ASN][1000 genomes]
rs11168797	0.90[ASN][1000 genomes]
rs11168798	0.83[ASN][1000 genomes]
rs11168800	0.83[ASN][1000 genomes]
rs11168801	0.83[ASN][1000 genomes]
rs11168803	0.89[ASN][1000 genomes]
rs11168811	0.81[ASN][1000 genomes]
rs11168812	0.88[ASN][1000 genomes]
rs11608916	0.94[ASN][1000 genomes]
rs11610459	0.95[ASN][1000 genomes]
rs11610497	0.95[ASN][1000 genomes]
rs11614474	0.95[ASN][1000 genomes]
rs12227240	0.95[ASN][1000 genomes]
rs12228521	0.97[ASN][1000 genomes]
rs12229275	0.92[ASN][1000 genomes]
rs12369505	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12423542	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12579249	0.95[ASN][1000 genomes]
rs1318692	0.97[ASN][1000 genomes]
rs1690182	0.88[ASN][1000 genomes]
rs1818996	0.90[ASN][1000 genomes]
rs1830192	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2030900	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2070940	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2073480	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2131713	0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2272311	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2272312	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2293449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2368701	0.97[ASN][1000 genomes]
rs2453063	0.89[ASN][1000 genomes]
rs2463175	0.88[ASN][1000 genomes]
rs2641450	0.86[ASN][1000 genomes]
rs2694839	0.88[ASN][1000 genomes]
rs2694840	0.86[ASN][1000 genomes]
rs3741627	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3759146	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3759148	1.00[ASW][hapmap]
rs3782353	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3809147	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3825182	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3825184	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4018510	0.90[ASN][1000 genomes]
rs4237854	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4433614	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4526804	0.88[ASN][1000 genomes]
rs4760600	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760661	0.94[ASN][1000 genomes]
rs4760663	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs4760664	0.88[ASN][1000 genomes]
rs4760665	0.97[ASN][1000 genomes]
rs4760666	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4760667	0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4760668	0.89[ASN][1000 genomes]
rs58023472	0.95[ASN][1000 genomes]
rs59087236	0.88[ASN][1000 genomes]
rs61941142	0.97[ASN][1000 genomes]
rs61942166	0.88[ASN][1000 genomes]
rs61942167	0.90[ASN][1000 genomes]
rs61942169	0.89[ASN][1000 genomes]
rs61942207	0.88[ASN][1000 genomes]
rs61942209	0.82[ASN][1000 genomes]
rs6580696	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7297958	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7298330	0.95[ASN][1000 genomes]
rs7304942	0.95[ASN][1000 genomes]
rs7313988	0.88[ASN][1000 genomes]
rs7489036	0.92[ASN][1000 genomes]
rs7963018	0.89[ASN][1000 genomes]
rs7963160	0.88[ASN][1000 genomes]
rs7976473	0.88[ASN][1000 genomes]
rs833820	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs833821	0.90[ASN][1000 genomes]
rs833822	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs833827	0.88[ASN][1000 genomes]
rs833828	0.86[ASN][1000 genomes]
rs833839	0.83[ASN][1000 genomes]
rs833840	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs833841	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs833842	0.83[ASN][1000 genomes]
rs833843	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs961320	0.97[ASN][1000 genomes]
rs9645813	0.82[ASN][1000 genomes]
rs9706255	1.00[ASW][hapmap]
rs9783452	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9783477	0.88[ASN][1000 genomes]
rs9788029	0.97[ASN][1000 genomes]
rs9795742	0.93[ASN][1000 genomes]
rs9796008	0.95[ASN][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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10783289	FKBP11	cis	parietal	SCAN
rs10783289	FKBP11	cis	brain	BrainEAC
rs10783289	FKBP11	cis	cerebellum	SCAN
rs10783289	ZNF641	cis	cerebellum	SCAN
rs10783289	CCDC65	cis	brain	BrainEAC
rs10783289	AQP6	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49298200-49301000	Weak transcription	Liver	Liver
2	chr12:49298200-49315800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:49298200-49318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:49298400-49299400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:49298400-49299800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:49298400-49301000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:49298400-49301000	Weak transcription	Fetal Intestine Small	intestine
8	chr12:49298400-49301000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:49298400-49301200	Weak transcription	Fetal Intestine Large	intestine
10	chr12:49298400-49308000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:49298400-49310400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:49298400-49310400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:49298400-49310400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:49298400-49310600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:49298400-49310600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:49298400-49310800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:49298400-49310800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:49298400-49311400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:49298400-49313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:49298400-49314800	Weak transcription	Lung	lung
21	chr12:49298400-49315000	Weak transcription	Osteobl	bone
22	chr12:49298400-49317800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:49298400-49318000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:49298400-49318000	Weak transcription	Brain Substantia Nigra	brain
25	chr12:49298400-49318000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:49298400-49318200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:49298400-49318200	Weak transcription	Right Atrium	heart
28	chr12:49298400-49318400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:49298600-49299400	Bivalent Enhancer	HepG2	liver
30	chr12:49298600-49300800	Weak transcription	HSMMtube	muscle
31	chr12:49298600-49301000	Weak transcription	Fetal Kidney	kidney
32	chr12:49298600-49301000	Weak transcription	A549	lung
33	chr12:49298600-49310400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:49298600-49315000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:49298600-49315000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:49298600-49316000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:49298600-49318200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:49298800-49301400	Weak transcription	Gastric	stomach
39	chr12:49298800-49301400	Weak transcription	Pancreas	Pancrea
40	chr12:49298800-49307800	Weak transcription	Fetal Stomach	stomach
41	chr12:49298800-49308400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:49298800-49315400	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:49298800-49315800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:49298800-49318000	Weak transcription	Fetal Lung	lung
45	chr12:49298800-49318200	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links