Variant report

Variant	rs1007079
Chromosome Location	chr3:139149486-139149487
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	chr3:139149320..139150091-chr3:139238870..139239588,2	MCF-7	breast:
2	chr3:139146805..139148507-chr3:139148685..139150247,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11919679	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11924964	0.87[CEU][hapmap]
rs12107249	0.87[CEU][hapmap]
rs1599926	0.87[CEU][hapmap]
rs1602627	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs182409	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes]
rs188419	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs192688	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs211581	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs211584	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2233817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278577	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2307030	1.00[CEU][hapmap]
rs295475	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs295476	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295477	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3772874	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3772875	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821546	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60082560	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60961550	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6439863	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6776315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72986799	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7373142	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7373302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7648636	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649535	0.87[CEU][hapmap]
rs7651618	0.87[CEU][hapmap]
rs9819224	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9858740	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9859683	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9879736	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9879748	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9882253	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

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:54 , 50 per page) page: 1 2

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	chr3:139142800-139150400	Weak transcription	Spleen	Spleen
19	chr3:139142800-139162600	Weak transcription	Psoas Muscle	Psoas
20	chr3:139142800-139169000	Weak transcription	Aorta	Aorta
21	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
22	chr3:139143000-139153800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:139143400-139152000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:139143600-139153800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:139144800-139151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:139144800-139173200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:139145000-139153400	Weak transcription	Ovary	ovary
28	chr3:139145000-139153800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:139145200-139152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:139145200-139153200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:139145200-139158000	Weak transcription	Brain Substantia Nigra	brain
32	chr3:139145200-139158200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:139145200-139164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:139145200-139170400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:139145400-139153400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:139146600-139150600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:139146800-139153400	Weak transcription	Fetal Lung	lung
38	chr3:139147000-139149800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:139147200-139158200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:139147400-139149600	Weak transcription	Fetal Kidney	kidney
41	chr3:139147400-139153000	Weak transcription	Fetal Intestine Large	intestine
42	chr3:139147400-139153000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:139147400-139160200	Weak transcription	Brain Angular Gyrus	brain
44	chr3:139147800-139153200	Weak transcription	Fetal Intestine Small	intestine
45	chr3:139148000-139160000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:139148800-139150600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:139148800-139153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:139149400-139149600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:139149400-139149600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:139149400-139149600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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