Variant report

Variant	rs3789139
Chromosome Location	chr4:121675253-121675254
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10006287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10026533	0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1015219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs1033096	0.86[ASN][1000 genomes]
rs10518380	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs11943025	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12499586	0.88[EUR][1000 genomes]
rs12499872	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12507367	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12513227	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs12639772	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12644850	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1397768	1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1397769	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1397771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1397773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1397774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1450461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs1463785	0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1496260	0.86[ASN][1000 genomes]
rs1511302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1511311	0.82[ASN][1000 genomes]
rs1588524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes]
rs1597491	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs168226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs17051240	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17051244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17051252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17051254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17051259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17051275	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs171068	0.80[AMR][1000 genomes]
rs1809075	0.80[AMR][1000 genomes]
rs1849075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1849076	0.85[ASN][1000 genomes]
rs2136999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167208	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2667171	0.80[AMR][1000 genomes]
rs28488919	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28810489	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs343182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs343185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs343189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs3804170	0.83[EUR][1000 genomes]
rs3827584	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4833182	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4833670	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4833671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833689	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs6813562	0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6855578	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs72678303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72678309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72678319	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72678324	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72678335	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72680418	0.83[AMR][1000 genomes]
rs896060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs994831	0.91[CHB][hapmap]

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	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1004485	chr4:121542992-121716769	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916737	chr4:121589793-121748847	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv461634	chr4:121623057-121765527	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv595334	chr4:121623057-121765527	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121652600-121687000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:121668400-121690400	Weak transcription	Osteobl	bone
3	chr4:121671800-121684200	Weak transcription	Ovary	ovary
4	chr4:121671800-121697000	Weak transcription	Pancreas	Pancrea
5	chr4:121671800-121728600	Weak transcription	Left Ventricle	heart
6	chr4:121672000-121676600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:121672000-121722400	Weak transcription	Right Ventricle	heart
8	chr4:121672400-121675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:121672400-121676800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:121672400-121680800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:121672400-121690400	Weak transcription	Lung	lung
12	chr4:121672400-121728800	Weak transcription	Aorta	Aorta
13	chr4:121672400-121728800	Weak transcription	Fetal Stomach	stomach
14	chr4:121673000-121675400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:121673000-121678200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:121673000-121690200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:121673000-121697200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:121673000-121705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:121673000-121722400	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:121673000-121737400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:121673200-121685600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:121673200-121690400	Weak transcription	Fetal Lung	lung
23	chr4:121673400-121678200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:121673400-121690400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:121673600-121692800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:121674400-121676600	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr4:121674600-121676000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:121674600-121676800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:121674600-121677200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:121674800-121676200	Enhancers	Fetal Heart	heart
31	chr4:121675000-121675400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr4:121675000-121675400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:121675000-121675400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr4:121675000-121675400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr4:121675000-121675400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:121675000-121675400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr4:121675000-121675400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr4:121675000-121675400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:121675000-121676000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:121675000-121676000	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr4:121675200-121675800	Weak transcription	Fetal Intestine Large	intestine
42	chr4:121675200-121677000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:121675200-121678800	Weak transcription	Fetal Intestine Small	intestine

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