Variant report

Variant	rs4678415
Chromosome Location	chr3:138086635-138086636
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138081144..138083981-chr3:138086003..138087797,3	MCF-7	breast:
2	chr3:138084125..138087091-chr3:138095064..138097156,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1002766	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1092338	0.82[ASN][1000 genomes]
rs11710280	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11713141	0.84[EUR][1000 genomes]
rs1199330	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1199331	0.87[EUR][1000 genomes]
rs1199332	0.90[CHD][hapmap]
rs1199337	0.83[ASN][1000 genomes]
rs1199338	0.93[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12107581	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490350	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13324341	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs1564407	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564408	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678440	0.83[ASN][1000 genomes]
rs1679147	0.92[EUR][1000 genomes]
rs1720819	0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs1720828	0.90[CHD][hapmap]
rs185244	0.83[ASN][1000 genomes]
rs1904349	0.81[ASN][1000 genomes]
rs2054468	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061936	0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2169973	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2293252	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs253665	0.84[CHD][hapmap]
rs35219044	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755751	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773752	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773758	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773759	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816730	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40593	0.87[CHD][hapmap]
rs4678260	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678261	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678407	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4678408	0.89[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4678409	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678410	0.92[EUR][1000 genomes]
rs4678411	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678412	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678417	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439804	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439805	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439806	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6439807	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67559768	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6766859	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6769236	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769261	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782181	0.89[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6782449	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784989	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789235	0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6790398	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6802211	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6807945	0.84[CHD][hapmap]
rs730158	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731632	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751357	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615658	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626388	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626424	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637666	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639809	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639850	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642400	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289559	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs940233	0.86[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9825697	0.87[EUR][1000 genomes]
rs9834911	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9845672	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846198	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846223	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854465	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855722	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138068800-138093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:138069200-138088200	Weak transcription	Fetal Lung	lung
3	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
4	chr3:138071200-138096600	Weak transcription	Aorta	Aorta
5	chr3:138074200-138095600	Enhancers	Fetal Heart	heart
6	chr3:138074800-138089800	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:138075000-138090000	Enhancers	Brain Anterior Caudate	brain
8	chr3:138075400-138087400	Enhancers	Right Atrium	heart
9	chr3:138075600-138089400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:138077800-138091600	Enhancers	Right Ventricle	heart
12	chr3:138078600-138100600	Weak transcription	NH-A	brain
13	chr3:138079600-138095600	Weak transcription	Fetal Brain Female	brain
14	chr3:138080200-138096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:138080600-138092000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:138081000-138088400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:138081200-138087000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:138081600-138091000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:138082200-138087400	Enhancers	Ovary	ovary
21	chr3:138082200-138088200	Genic enhancers	HSMMtube	muscle
22	chr3:138082400-138088800	Enhancers	Spleen	Spleen
23	chr3:138082400-138089400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:138082800-138088400	Genic enhancers	HSMM	muscle
25	chr3:138082800-138089400	Enhancers	Brain Hippocampus Middle	brain
26	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:138083200-138091800	Enhancers	Adipose Nuclei	Adipose
28	chr3:138083200-138091800	Enhancers	Left Ventricle	heart
29	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:138083400-138087200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:138083400-138090400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:138083800-138089400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:138084200-138087200	Enhancers	Psoas Muscle	Psoas
34	chr3:138084200-138089600	Enhancers	Lung	lung
35	chr3:138084400-138087200	Enhancers	Fetal Muscle Leg	muscle
36	chr3:138084400-138087600	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:138084400-138089600	Enhancers	Brain Substantia Nigra	brain
38	chr3:138084600-138087000	Enhancers	Placenta	Placenta
39	chr3:138084800-138087000	Enhancers	Fetal Muscle Trunk	muscle
40	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:138085600-138089000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:138085600-138091000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:138085800-138086800	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:138085800-138096200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:138086200-138087000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr3:138086200-138089400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:138086200-138100400	Weak transcription	HepG2	liver
48	chr3:138086400-138086800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr3:138086400-138087000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:138086400-138087200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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