Variant report

Variant	rs13074317
Chromosome Location	chr3:138100253-138100254
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	chr3:138099681..138102999-chr3:138104936..138107535,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513053	0.89[JPT][hapmap]
rs1092338	0.91[EUR][1000 genomes]
rs1199330	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12695685	0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs13079209	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080413	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083299	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13096934	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1678440	0.91[EUR][1000 genomes]
rs1720819	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2279241	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2291127	1.00[ASN][1000 genomes]
rs2293251	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2306374	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2347252	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34078858	0.84[ASN][1000 genomes]
rs34140440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34568901	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34905952	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3732837	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3773750	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59217491	0.84[ASN][1000 genomes]
rs9818870	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9828345	1.00[JPT][hapmap]
rs9848655	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9851766	1.00[ASN][1000 genomes]
rs9864898	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9872754	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1797142	chr3:138087467-138122781	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:138078600-138100600	Weak transcription	NH-A	brain
3	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:138086200-138100400	Weak transcription	HepG2	liver
7	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
10	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
11	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:138091200-138100400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:138091400-138100800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:138093600-138100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:138093800-138100400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:138094600-138100600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:138097000-138100400	Weak transcription	Fetal Brain Male	brain
19	chr3:138097600-138100400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:138097600-138100400	Weak transcription	Fetal Stomach	stomach
21	chr3:138097600-138100400	Weak transcription	Osteobl	bone
22	chr3:138097600-138100600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:138097600-138116000	Weak transcription	Aorta	Aorta
24	chr3:138097600-138116600	Weak transcription	Brain Germinal Matrix	brain
25	chr3:138097800-138100400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:138098000-138100600	Weak transcription	Fetal Brain Female	brain
27	chr3:138098200-138104200	Enhancers	Fetal Heart	heart
28	chr3:138098400-138103800	Enhancers	Brain Substantia Nigra	brain
29	chr3:138098600-138102600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr3:138099200-138104000	Enhancers	Right Ventricle	heart
31	chr3:138099600-138103200	Enhancers	Brain Hippocampus Middle	brain
32	chr3:138099600-138105200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:138099800-138101800	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:138099800-138102000	Genic enhancers	HSMM	muscle
35	chr3:138099800-138103800	Enhancers	Adipose Nuclei	Adipose
36	chr3:138099800-138103800	Enhancers	Brain Anterior Caudate	brain
37	chr3:138099800-138103800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:138099800-138103800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:138099800-138104000	Enhancers	Left Ventricle	heart
40	chr3:138099800-138104200	Enhancers	Placenta	Placenta
41	chr3:138099800-138104200	Enhancers	Right Atrium	heart
42	chr3:138100000-138100400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:138100000-138100400	Genic enhancers	Pancreas	Pancrea
44	chr3:138100000-138100600	Enhancers	Stomach Smooth Muscle	stomach
45	chr3:138100000-138101600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:138100000-138101600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr3:138100000-138101800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr3:138100000-138102600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:138100000-138102600	Enhancers	Colon Smooth Muscle	Colon
50	chr3:138100000-138103600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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