Variant report

Variant	rs3898712
Chromosome Location	chr12:31671240-31671241
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	chr12:31664969..31667862-chr12:31670364..31672875,3	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10771826	0.84[EUR][1000 genomes]
rs10771830	0.89[EUR][1000 genomes]
rs10771831	0.86[EUR][1000 genomes]
rs10771833	0.92[EUR][1000 genomes]
rs10771834	0.86[EUR][1000 genomes]
rs10771835	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10771837	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843937	0.85[EUR][1000 genomes]
rs10843938	0.85[EUR][1000 genomes]
rs10843939	0.86[EUR][1000 genomes]
rs10843953	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843954	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843957	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843962	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843966	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843968	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843969	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843971	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843972	0.83[EUR][1000 genomes]
rs11051417	0.85[EUR][1000 genomes]
rs11051427	0.87[EUR][1000 genomes]
rs11051428	0.88[EUR][1000 genomes]
rs11051440	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11051446	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051454	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051461	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051467	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051472	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051476	0.84[EUR][1000 genomes]
rs1150948	0.88[ASN][1000 genomes]
rs1150949	0.95[ASN][1000 genomes]
rs12368987	0.84[EUR][1000 genomes]
rs12369701	0.99[ASN][1000 genomes]
rs12371432	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259360	0.95[ASN][1000 genomes]
rs1268747	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560634	0.83[EUR][1000 genomes]
rs16918740	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1879385	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2163730	0.87[EUR][1000 genomes]
rs2351921	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2351922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2351923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892638	0.84[EUR][1000 genomes]
rs34498192	0.90[EUR][1000 genomes]
rs3741877	0.85[EUR][1000 genomes]
rs3741878	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3803114	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3850966	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3887250	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4930979	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931499	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4931511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61097018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918606	0.86[EUR][1000 genomes]
rs61930275	0.84[EUR][1000 genomes]
rs6487990	0.84[EUR][1000 genomes]
rs6487991	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487995	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7132688	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136559	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7297507	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297997	0.87[EUR][1000 genomes]
rs7299425	0.83[EUR][1000 genomes]
rs7300106	0.88[EUR][1000 genomes]
rs7301326	0.86[EUR][1000 genomes]
rs7302695	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73080572	0.86[EUR][1000 genomes]
rs7308202	0.89[EUR][1000 genomes]
rs7311970	0.84[EUR][1000 genomes]
rs7313889	0.86[EUR][1000 genomes]
rs7314404	0.87[EUR][1000 genomes]
rs7314739	0.86[EUR][1000 genomes]
rs7960380	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963764	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7978277	0.84[EUR][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	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	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31658800-31671600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:31660000-31674600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:31662200-31671600	Weak transcription	HepG2	liver
4	chr12:31663600-31672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:31665000-31671400	Weak transcription	GM12878-XiMat	blood
6	chr12:31667800-31675400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:31667800-31687600	Weak transcription	Pancreas	Pancrea
8	chr12:31669200-31671400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:31669800-31671800	Enhancers	Brain Germinal Matrix	brain
10	chr12:31669800-31672000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:31669800-31673600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:31669800-31677800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:31670000-31671600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:31670000-31671600	Flanking Active TSS	A549	lung
15	chr12:31670000-31672000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr12:31670000-31672000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr12:31670000-31672000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:31670000-31673200	Enhancers	NHLF	lung
19	chr12:31670000-31673400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr12:31670000-31673400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:31670000-31674800	Enhancers	HUVEC	blood vessel
22	chr12:31670000-31675400	Enhancers	Fetal Kidney	kidney
23	chr12:31670000-31675400	Enhancers	Fetal Lung	lung
24	chr12:31670000-31676400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:31670200-31671400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:31670200-31671400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:31670200-31671400	Enhancers	HSMMtube	muscle
28	chr12:31670200-31671800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:31670200-31672000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:31670200-31672000	Enhancers	HSMM	muscle
31	chr12:31670200-31672000	Enhancers	NHDF-Ad	bronchial
32	chr12:31670200-31672200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:31670200-31672200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:31670200-31672600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:31670200-31673000	Enhancers	H9 Cell Line	embryonic stem cell
36	chr12:31670200-31673000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:31670200-31673000	Enhancers	Brain Cingulate Gyrus	brain
38	chr12:31670200-31673000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr12:31670200-31673000	Enhancers	Fetal Brain Female	brain
40	chr12:31670200-31673000	Enhancers	Ovary	ovary
41	chr12:31670200-31673200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr12:31670200-31673200	Enhancers	Primary B cells from peripheral blood	blood
43	chr12:31670200-31673200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr12:31670200-31673400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr12:31670200-31673400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:31670200-31673400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:31670200-31673400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:31670200-31673400	Enhancers	Osteobl	bone
49	chr12:31670200-31676800	Enhancers	Fetal Heart	heart
50	chr12:31670400-31671400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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