Variant report

Variant	rs12820673
Chromosome Location	chr12:29711631-29711632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10400534	0.91[ASN][1000 genomes]
rs10400541	0.86[ASN][1000 genomes]
rs10771545	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771546	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771547	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771549	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843443	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843446	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050270	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050271	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050273	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050278	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050280	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050281	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050284	0.93[ASN][1000 genomes]
rs11050288	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050291	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050292	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11050293	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050295	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050296	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050297	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050298	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11050299	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050300	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050301	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050302	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11611194	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12371221	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12581671	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12810291	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1326758	0.84[ASN][1000 genomes]
rs159696	0.86[ASN][1000 genomes]
rs159701	0.83[ASN][1000 genomes]
rs159703	0.82[ASN][1000 genomes]
rs159704	0.82[ASN][1000 genomes]
rs159705	0.82[ASN][1000 genomes]
rs1988548	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060569	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2113879	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2113880	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288131	0.81[ASN][1000 genomes]
rs2288132	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288133	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288230	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2350532	0.88[EUR][1000 genomes]
rs299444	0.86[ASN][1000 genomes]
rs299445	0.86[ASN][1000 genomes]
rs299455	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs299456	0.83[ASN][1000 genomes]
rs299457	0.83[ASN][1000 genomes]
rs299459	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299462	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs299463	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs299464	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs299465	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs299466	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs299472	0.93[EUR][1000 genomes]
rs299475	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34020170	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34187264	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34555972	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35111056	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35536095	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35741143	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs375109	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4931201	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4931204	0.93[ASN][1000 genomes]
rs60500145	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487837	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7294502	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7301491	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7306397	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310555	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310895	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7314549	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7971202	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9300191	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9300192	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9738399	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:29698200-29712600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:29699400-29715800	Weak transcription	Right Ventricle	heart
5	chr12:29700000-29712000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:29700200-29712200	Weak transcription	Ovary	ovary
7	chr12:29700400-29712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
10	chr12:29701000-29714200	Weak transcription	HSMMtube	muscle
11	chr12:29701200-29714400	Weak transcription	NHDF-Ad	bronchial
12	chr12:29701200-29714400	Weak transcription	NHLF	lung
13	chr12:29701200-29715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:29701200-29715600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:29703800-29715200	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:29705000-29716000	Weak transcription	Spleen	Spleen
17	chr12:29706000-29715200	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:29706200-29715000	Weak transcription	Osteobl	bone
19	chr12:29706600-29716200	Weak transcription	Aorta	Aorta
20	chr12:29706800-29712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:29706800-29712200	Weak transcription	Liver	Liver
22	chr12:29707400-29712200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:29707400-29714600	Weak transcription	Fetal Heart	heart
24	chr12:29707800-29712600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:29709800-29711800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:29709800-29756200	Weak transcription	HMEC	breast
27	chr12:29710000-29711800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:29710000-29712200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:29710000-29713800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:29710000-29714200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:29710000-29714200	Weak transcription	HSMM	muscle
32	chr12:29710000-29715000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:29710000-29715600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:29710200-29711800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:29710200-29717800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:29710600-29711800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:29711200-29712000	Weak transcription	Fetal Kidney	kidney
38	chr12:29711400-29713200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:29711400-29716600	Enhancers	Stomach Mucosa	stomach
40	chr12:29711400-29718200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr12:29711600-29711800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr12:29711600-29711800	Enhancers	Right Atrium	heart
43	chr12:29711600-29711800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr12:29711600-29712000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:29711600-29712000	Enhancers	Adipose Nuclei	Adipose
46	chr12:29711600-29712000	Enhancers	Duodenum Mucosa	Duodenum
47	chr12:29711600-29712000	Genic enhancers	Left Ventricle	heart
48	chr12:29711600-29712000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:29711600-29712200	Strong transcription	Hela-S3	cervix
50	chr12:29711600-29712400	Enhancers	Rectal Mucosa Donor 31	rectum

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