Variant report

Variant	rs1678440
Chromosome Location	chr3:138099905-138099906
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	chr3:138099681..138102999-chr3:138104936..138107535,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1002766	0.81[ASN][1000 genomes]
rs1092338	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1199329	0.82[ASN][1000 genomes]
rs1199330	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199337	0.98[ASN][1000 genomes]
rs1199338	0.99[ASN][1000 genomes]
rs1199340	0.81[ASN][1000 genomes]
rs12107581	0.84[ASN][1000 genomes]
rs12490350	0.84[ASN][1000 genomes]
rs13074317	0.91[EUR][1000 genomes]
rs13079209	0.91[EUR][1000 genomes]
rs13080413	0.87[EUR][1000 genomes]
rs13324341	0.97[ASN][1000 genomes]
rs1564407	0.83[ASN][1000 genomes]
rs1564408	0.81[ASN][1000 genomes]
rs1678442	0.82[ASN][1000 genomes]
rs1678443	0.82[ASN][1000 genomes]
rs1720819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720823	0.82[ASN][1000 genomes]
rs1720828	0.81[ASN][1000 genomes]
rs185244	1.00[ASN][1000 genomes]
rs2061936	0.87[ASN][1000 genomes]
rs2293252	0.85[ASN][1000 genomes]
rs253661	0.82[ASN][1000 genomes]
rs253663	0.81[ASN][1000 genomes]
rs34140440	0.91[EUR][1000 genomes]
rs34568901	0.88[EUR][1000 genomes]
rs3773750	0.88[EUR][1000 genomes]
rs3773752	0.83[ASN][1000 genomes]
rs3773758	0.82[ASN][1000 genomes]
rs3773759	0.83[ASN][1000 genomes]
rs3816730	0.83[ASN][1000 genomes]
rs4678260	0.84[ASN][1000 genomes]
rs4678261	0.84[ASN][1000 genomes]
rs4678412	0.83[ASN][1000 genomes]
rs4678415	0.83[ASN][1000 genomes]
rs4678417	0.84[ASN][1000 genomes]
rs6439807	0.83[ASN][1000 genomes]
rs6782181	0.93[ASN][1000 genomes]
rs6789235	0.93[ASN][1000 genomes]
rs6807945	0.89[ASN][1000 genomes]
rs730158	0.83[ASN][1000 genomes]
rs731632	0.83[ASN][1000 genomes]
rs751357	0.83[ASN][1000 genomes]
rs7626388	0.83[ASN][1000 genomes]
rs7626424	0.83[ASN][1000 genomes]
rs7639809	0.83[ASN][1000 genomes]
rs7639850	0.83[ASN][1000 genomes]
rs7642400	0.87[ASN][1000 genomes]
rs774009	0.82[ASN][1000 genomes]
rs9289559	0.84[ASN][1000 genomes]
rs940233	0.82[ASN][1000 genomes]
rs9855722	0.82[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:66 , 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	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:138086200-138100400	Weak transcription	HepG2	liver
8	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:138087200-138100000	Weak transcription	Pancreas	Pancrea
10	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:138089200-138100000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
13	chr3:138089400-138100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:138089400-138100000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
16	chr3:138089600-138100200	Weak transcription	Lung	lung
17	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:138091200-138100400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr3:138091400-138100800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:138093600-138100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:138093800-138100000	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:138093800-138100400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:138094400-138100200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:138094600-138100600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:138094800-138100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:138097000-138100400	Weak transcription	Fetal Brain Male	brain
28	chr3:138097400-138100200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:138097400-138100200	Weak transcription	Psoas Muscle	Psoas
30	chr3:138097600-138100000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:138097600-138100200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:138097600-138100200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:138097600-138100200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:138097600-138100200	Weak transcription	Ovary	ovary
35	chr3:138097600-138100400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:138097600-138100400	Weak transcription	Fetal Stomach	stomach
37	chr3:138097600-138100400	Weak transcription	Osteobl	bone
38	chr3:138097600-138100600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:138097600-138116000	Weak transcription	Aorta	Aorta
40	chr3:138097600-138116600	Weak transcription	Brain Germinal Matrix	brain
41	chr3:138097800-138100000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:138097800-138100000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:138097800-138100200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:138097800-138100400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:138098000-138100000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:138098000-138100000	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:138098000-138100600	Weak transcription	Fetal Brain Female	brain
48	chr3:138098200-138104200	Enhancers	Fetal Heart	heart
49	chr3:138098400-138103800	Enhancers	Brain Substantia Nigra	brain
50	chr3:138098600-138102600	Enhancers	Brain Inferior Temporal Lobe	brain

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