Variant report

Variant	rs12054428
Chromosome Location	chr3:138179785-138179786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12630060	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630351	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632793	0.82[EUR][1000 genomes]
rs12633098	0.84[EUR][1000 genomes]
rs12635354	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12635490	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635904	0.82[EUR][1000 genomes]
rs12636936	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12637638	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12637679	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12638938	0.84[EUR][1000 genomes]
rs13059817	0.82[EUR][1000 genomes]
rs13073978	0.82[EUR][1000 genomes]
rs13084780	0.82[EUR][1000 genomes]
rs13098554	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546758	0.84[EUR][1000 genomes]
rs1563615	0.82[EUR][1000 genomes]
rs2085446	0.82[EUR][1000 genomes]
rs2085447	0.86[EUR][1000 genomes]
rs2280596	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34011134	0.82[EUR][1000 genomes]
rs34416776	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34482601	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34607531	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34640717	0.86[EUR][1000 genomes]
rs34878008	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35034861	0.82[EUR][1000 genomes]
rs35270255	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35340237	0.83[ASN][1000 genomes]
rs35537868	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35549884	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35597846	0.82[EUR][1000 genomes]
rs35834585	0.82[EUR][1000 genomes]
rs35876758	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56028542	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57516770	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58873565	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59184769	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60371967	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60426689	0.86[EUR][1000 genomes]
rs61258082	0.81[ASN][1000 genomes]
rs67666216	0.86[ASN][1000 genomes]
rs6768963	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6784770	0.81[ASN][1000 genomes]
rs7611650	0.87[EUR][1000 genomes]
rs774014	0.87[EUR][1000 genomes]
rs811794	0.84[EUR][1000 genomes]
rs812277	0.84[EUR][1000 genomes]
rs9049	0.82[EUR][1000 genomes];0.85[ASN][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	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr3:138155000-138182800	Weak transcription	Gastric	stomach
2	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:138166600-138183200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
6	chr3:138171200-138185400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:138172400-138181800	Weak transcription	Placenta	Placenta
9	chr3:138173800-138181200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:138174200-138180800	Enhancers	Fetal Muscle Trunk	muscle
11	chr3:138174600-138183600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:138175200-138180400	Weak transcription	Osteobl	bone
13	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:138175400-138180000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:138176400-138180000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:138176400-138180600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:138176400-138184800	Genic enhancers	Fetal Muscle Leg	muscle
18	chr3:138176800-138187200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:138177200-138181200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:138177600-138187200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:138177600-138195400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:138178000-138180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
25	chr3:138178400-138179800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:138178400-138183200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:138178600-138181200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:138178600-138182600	Weak transcription	Fetal Stomach	stomach
29	chr3:138178600-138187000	Weak transcription	Right Atrium	heart
30	chr3:138178800-138179800	Enhancers	Fetal Intestine Small	intestine
31	chr3:138178800-138188800	Weak transcription	Right Ventricle	heart
32	chr3:138179000-138179800	Genic enhancers	Lung	lung
33	chr3:138179000-138181000	Enhancers	HSMM	muscle
34	chr3:138179400-138180600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:138179600-138179800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:138179600-138180000	Strong transcription	Brain Angular Gyrus	brain
37	chr3:138179600-138180400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:138179600-138180600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:138179600-138180800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:138179600-138180800	Enhancers	NHDF-Ad	bronchial
41	chr3:138179600-138181200	Enhancers	HSMMtube	muscle

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