Variant report

Variant	rs12792306
Chromosome Location	chr11:71166992-71166993
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	chr11:71166687..71169492-chr11:71189793..71191469,2	MCF-7	breast:
2	chr11:71166959..71169196-chr11:71181524..71183295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172890	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1044482	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233746	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233747	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233789	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11546509	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600569	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600860	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603330	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604642	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606033	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606612	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606631	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278461	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419279	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419334	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422045	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785878	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789751	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790010	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790558	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12791871	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793224	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793530	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794668	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797951	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12800438	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803256	0.80[ASN][1000 genomes]
rs12806844	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807718	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807827	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12808368	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981412	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002063	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040323	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276360	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276361	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276362	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282620	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282621	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28364617	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2852853	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750997	0.87[EUR][1000 genomes]
rs3794060	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423214	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4488226	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944062	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944946	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944949	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944955	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944956	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944958	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944959	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944996	0.89[ASN][1000 genomes]
rs4945008	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732934	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928249	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935125	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938885	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7944926	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909217	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12792306	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs12792306	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12792306	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs12792306	RP11-660L16.2	cis	lung	GTEx
rs12792306	RP11-660L16.2	cis	Thyroid	GTEx
rs12792306	RP11-660L16.2	cis	Whole Blood	GTEx
rs12792306	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs12792306	NADSYN1	cis	lung	GTEx
rs12792306	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs12792306	RP11-660L16.2	cis	Artery Aorta	GTEx
rs12792306	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs12792306	NADSYN1	cis	Thyroid	GTEx
rs12792306	NADSYN1	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
2	chr11:71165200-71169800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:71165200-71169800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:71165200-71177400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:71165200-71177600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:71165200-71199200	Weak transcription	Right Atrium	heart
7	chr11:71165400-71170000	Weak transcription	Small Intestine	intestine
8	chr11:71165400-71194200	Weak transcription	Fetal Heart	heart
9	chr11:71165800-71167000	Weak transcription	NH-A	brain
10	chr11:71165800-71167200	Genic enhancers	Dnd41	blood
11	chr11:71165800-71168200	Strong transcription	Hela-S3	cervix
12	chr11:71165800-71168600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:71165800-71168800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:71165800-71169400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:71165800-71170000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:71165800-71171200	Strong transcription	K562	blood
17	chr11:71165800-71171800	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr11:71165800-71172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:71165800-71173000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:71165800-71174000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:71165800-71175800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:71165800-71178200	Strong transcription	NHLF	lung
23	chr11:71165800-71178400	Strong transcription	Fetal Stomach	stomach
24	chr11:71165800-71179200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:71165800-71179200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:71165800-71179200	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:71165800-71180400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:71166000-71168000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:71166000-71169400	Strong transcription	NHEK	skin
31	chr11:71166000-71169600	Strong transcription	Placenta	Placenta
32	chr11:71166000-71171400	Strong transcription	Brain Angular Gyrus	brain
33	chr11:71166000-71171600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr11:71166000-71171600	Strong transcription	Brain Germinal Matrix	brain
35	chr11:71166000-71172000	Strong transcription	Fetal Brain Female	brain
36	chr11:71166000-71173000	Strong transcription	Osteobl	bone
37	chr11:71166000-71173600	Strong transcription	HSMM	muscle
38	chr11:71166000-71173800	Strong transcription	Brain Substantia Nigra	brain
39	chr11:71166000-71175400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr11:71166000-71175600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:71166000-71176000	Strong transcription	Brain Anterior Caudate	brain
42	chr11:71166000-71178400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:71166000-71178600	Strong transcription	Primary T cells from cord blood	blood
44	chr11:71166000-71178600	Strong transcription	Spleen	Spleen
45	chr11:71166000-71179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:71166000-71180000	Strong transcription	A549	lung
47	chr11:71166000-71180200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:71166000-71180200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr11:71166000-71194200	Weak transcription	Fetal Brain Male	brain
50	chr11:71166200-71167200	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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