Variant report

Variant	rs6774691
Chromosome Location	chr3:139153935-139153936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139153603..139154270-chr3:139225278..139226293,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10513077	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11914638	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11924964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11928018	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12107249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1599926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs182409	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2233817	1.00[CEU][hapmap]
rs2278577	1.00[CEU][hapmap]
rs2289345	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289346	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2307030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34994114	0.81[ASN][1000 genomes]
rs3772874	1.00[CEU][hapmap]
rs3772875	0.87[CEU][hapmap]
rs56176652	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57459537	0.94[ASN][1000 genomes]
rs57490542	0.81[ASN][1000 genomes]
rs60077646	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61613815	0.81[ASN][1000 genomes]
rs6439863	1.00[CEU][hapmap]
rs6767503	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773840	0.88[ASN][1000 genomes]
rs6776315	1.00[CEU][hapmap]
rs6781318	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788896	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797945	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804069	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72986758	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7373302	1.00[CEU][hapmap]
rs7612306	0.82[ASN][1000 genomes]
rs7619827	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7622961	1.00[JPT][hapmap]
rs7644878	0.82[AMR][1000 genomes]
rs7649535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9756378	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9879736	1.00[CEU][hapmap]
rs9879748	1.00[CEU][hapmap]

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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2760754	chr3:139144615-139164874	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139136400-139166200	Weak transcription	Fetal Brain Female	brain
2	chr3:139138600-139166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:139138600-139170400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:139139600-139160000	Weak transcription	Fetal Brain Male	brain
5	chr3:139141200-139160000	Weak transcription	Lung	lung
6	chr3:139141400-139167000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:139142200-139172200	Weak transcription	Fetal Heart	heart
8	chr3:139142400-139154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:139142600-139158200	Weak transcription	Gastric	stomach
10	chr3:139142800-139162600	Weak transcription	Psoas Muscle	Psoas
11	chr3:139142800-139169000	Weak transcription	Aorta	Aorta
12	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
13	chr3:139144800-139173200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:139145200-139158000	Weak transcription	Brain Substantia Nigra	brain
15	chr3:139145200-139158200	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:139145200-139164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:139145200-139170400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:139147200-139158200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:139147400-139160200	Weak transcription	Brain Angular Gyrus	brain
20	chr3:139148000-139160000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:139149800-139170600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:139151800-139158200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:139152200-139159800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:139152800-139154600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:139152800-139154800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:139152800-139154800	Enhancers	Placenta	Placenta
27	chr3:139153000-139154200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:139153000-139154200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr3:139153000-139154400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:139153000-139154400	Enhancers	Fetal Intestine Large	intestine
31	chr3:139153200-139154200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:139153200-139154200	Enhancers	Duodenum Mucosa	Duodenum
33	chr3:139153200-139154200	Enhancers	Esophagus	oesophagus
34	chr3:139153200-139154200	Enhancers	NHDF-Ad	bronchial
35	chr3:139153200-139154400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:139153200-139154400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:139153200-139154400	Enhancers	Hela-S3	cervix
38	chr3:139153200-139154600	Enhancers	Adipose Nuclei	Adipose
39	chr3:139153200-139154600	Enhancers	HSMMtube	muscle
40	chr3:139153200-139154800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:139153400-139154000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:139153400-139154200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:139153400-139154200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:139153400-139154200	Genic enhancers	Ovary	ovary
45	chr3:139153400-139154400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr3:139153400-139154400	Enhancers	Fetal Lung	lung
47	chr3:139153400-139154400	Enhancers	HSMM	muscle
48	chr3:139153600-139154000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:139153600-139154000	Enhancers	NHEK	skin
50	chr3:139153600-139154200	Enhancers	HUES6 Cell Line	embryonic stem cell

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