Variant report

Variant	rs12809140
Chromosome Location	chr12:31686992-31686993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs12812075	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12816170	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12816386	0.83[EUR][1000 genomes]
rs12818749	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12819062	0.84[EUR][1000 genomes]
rs12820294	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12821808	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12822601	0.87[EUR][1000 genomes]
rs12825207	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12826193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12831480	0.83[EUR][1000 genomes]
rs16918738	0.92[ASN][1000 genomes]
rs16918744	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16918795	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs17497517	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17497656	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17497998	0.81[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2126897	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2271983	1.00[CHB][hapmap]
rs34007930	0.83[EUR][1000 genomes]
rs34094545	0.85[EUR][1000 genomes]
rs34184789	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34271764	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34308937	0.84[EUR][1000 genomes]
rs34450466	0.92[EUR][1000 genomes]
rs34585237	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34642866	0.83[EUR][1000 genomes]
rs34667511	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34949976	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34955459	0.84[EUR][1000 genomes]
rs34986122	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35029695	0.86[EUR][1000 genomes]
rs35193529	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35545963	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35567364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35679974	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35692484	0.86[EUR][1000 genomes]
rs3850967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4338625	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4421825	1.00[CHB][hapmap]
rs4930977	0.87[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4930981	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930983	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4931498	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4931503	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4931504	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4931510	0.81[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4931518	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55635343	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55643034	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55771933	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56183451	0.83[EUR][1000 genomes]
rs56234529	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56282720	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56409505	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66479670	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66520413	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66552209	0.85[EUR][1000 genomes]
rs66597773	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66635949	0.90[EUR][1000 genomes]
rs67415228	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67963293	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs68030436	0.81[EUR][1000 genomes]
rs71455664	0.85[EUR][1000 genomes]
rs71455667	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71455668	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71455669	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71455670	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71455671	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73080503	0.86[EUR][1000 genomes]
rs73084486	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73086471	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088505	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088597	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31667800-31687600	Weak transcription	Pancreas	Pancrea
2	chr12:31673400-31688400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:31675600-31689000	Weak transcription	Small Intestine	intestine
4	chr12:31679000-31688800	Weak transcription	Psoas Muscle	Psoas
5	chr12:31679000-31691400	Weak transcription	Fetal Intestine Large	intestine
6	chr12:31679400-31687600	Weak transcription	Primary B cells from cord blood	blood
7	chr12:31679800-31692000	Weak transcription	GM12878-XiMat	blood
8	chr12:31680600-31687800	Weak transcription	Left Ventricle	heart
9	chr12:31681200-31691000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:31681200-31691600	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:31683600-31687000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:31684400-31687200	Enhancers	Osteobl	bone
13	chr12:31684600-31687000	Enhancers	Hela-S3	cervix
14	chr12:31684800-31690600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:31685200-31688800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:31685400-31691000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:31685400-31691600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:31685400-31700600	Weak transcription	Aorta	Aorta
19	chr12:31685400-31708600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:31685600-31690000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:31685800-31687000	Enhancers	HepG2	liver
22	chr12:31686000-31688200	Weak transcription	Right Ventricle	heart
23	chr12:31686400-31687000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:31686600-31687000	Enhancers	Brain Anterior Caudate	brain
25	chr12:31686600-31687000	Flanking Active TSS	A549	lung
26	chr12:31686600-31687800	Weak transcription	Ovary	ovary
27	chr12:31686600-31688400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:31686600-31688800	Weak transcription	Adipose Nuclei	Adipose
29	chr12:31686800-31687800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr12:31686800-31688000	Weak transcription	Stomach Mucosa	stomach
31	chr12:31686800-31688200	Weak transcription	Fetal Heart	heart
32	chr12:31686800-31688400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:31686800-31688800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:31686800-31689000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:31686800-31689400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:31686800-31689400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:31686800-31689600	Weak transcription	Liver	Liver
38	chr12:31686800-31689800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:31686800-31690400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:31686800-31693200	Weak transcription	Fetal Intestine Small	intestine
41	chr12:31686800-31695600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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