Variant report

Variant	rs6788896
Chromosome Location	chr3:139151203-139151204
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	chr3:139141697..139144068-chr3:139149999..139151730,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10513077	0.97[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	0.94[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];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs182409	1.00[JPT][hapmap]
rs2233817	0.85[CEU][hapmap]
rs2278577	0.87[CEU][hapmap]
rs2289345	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289346	0.96[AFR][1000 genomes];1.00[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];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34994114	0.81[ASN][1000 genomes]
rs3772874	0.87[CEU][hapmap]
rs56176652	0.94[AFR][1000 genomes];1.00[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	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61613815	0.81[ASN][1000 genomes]
rs6439863	0.87[CEU][hapmap]
rs6767503	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773840	0.88[ASN][1000 genomes]
rs6774691	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781318	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804069	0.91[AMR][1000 genomes]
rs72986758	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7373302	0.87[CEU][hapmap]
rs7612306	0.82[ASN][1000 genomes]
rs7619827	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7622961	1.00[JPT][hapmap]
rs7644878	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7649535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.94[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];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9756378	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9879736	1.00[CEU][hapmap]
rs9879748	0.87[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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139114200-139153800	Weak transcription	Left Ventricle	heart
2	chr3:139136400-139166200	Weak transcription	Fetal Brain Female	brain
3	chr3:139137800-139153200	Weak transcription	Esophagus	oesophagus
4	chr3:139138200-139153600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:139138600-139166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:139138600-139170400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:139139600-139160000	Weak transcription	Fetal Brain Male	brain
8	chr3:139140800-139152800	Weak transcription	Placenta	Placenta
9	chr3:139140800-139153200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:139140800-139153200	Weak transcription	HSMMtube	muscle
11	chr3:139140800-139153800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:139141200-139160000	Weak transcription	Lung	lung
13	chr3:139141400-139167000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:139142200-139152800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:139142200-139172200	Weak transcription	Fetal Heart	heart
16	chr3:139142400-139154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:139142600-139158200	Weak transcription	Gastric	stomach
18	chr3:139142800-139162600	Weak transcription	Psoas Muscle	Psoas
19	chr3:139142800-139169000	Weak transcription	Aorta	Aorta
20	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
21	chr3:139143000-139153800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:139143400-139152000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:139143600-139153800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:139144800-139151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:139144800-139173200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:139145000-139153400	Weak transcription	Ovary	ovary
27	chr3:139145000-139153800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:139145200-139152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:139145200-139153200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:139145200-139158000	Weak transcription	Brain Substantia Nigra	brain
31	chr3:139145200-139158200	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:139145200-139164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:139145200-139170400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:139145400-139153400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:139146800-139153400	Weak transcription	Fetal Lung	lung
36	chr3:139147200-139158200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:139147400-139153000	Weak transcription	Fetal Intestine Large	intestine
38	chr3:139147400-139153000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:139147400-139160200	Weak transcription	Brain Angular Gyrus	brain
40	chr3:139147800-139153200	Weak transcription	Fetal Intestine Small	intestine
41	chr3:139148000-139160000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:139148800-139153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:139149600-139152800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:139149800-139153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:139149800-139170600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:139150600-139152200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:139151000-139151600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links