Variant report

Variant	rs4678417
Chromosome Location	chr3:138096512-138096513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138089900..138093622-chr3:138093776..138096723,3	MCF-7	breast:
2	chr3:138094416..138096515-chr3:138105748..138108016,2	MCF-7	breast:
3	chr3:138084125..138087091-chr3:138095064..138097156,2	K562	blood:
4	chr3:138093996..138096598-chr4:123678799..123680914,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1002766	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1092338	0.83[ASN][1000 genomes]
rs11710280	0.91[EUR][1000 genomes]
rs11713141	0.81[EUR][1000 genomes]
rs1199330	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1199331	0.91[EUR][1000 genomes]
rs1199337	0.82[ASN][1000 genomes]
rs1199338	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12107581	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490350	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324341	0.81[ASN][1000 genomes]
rs1564407	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1564408	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1678440	0.84[ASN][1000 genomes]
rs1679147	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1720819	0.84[ASN][1000 genomes]
rs185244	0.84[ASN][1000 genomes]
rs1904349	0.80[ASN][1000 genomes]
rs2054468	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2061936	0.92[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2169973	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293252	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35219044	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755751	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773752	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773758	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773759	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816730	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678261	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678407	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678408	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs4678409	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678410	0.88[EUR][1000 genomes]
rs4678411	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4678412	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678415	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	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439805	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439806	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs6439807	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67559768	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766859	0.83[EUR][1000 genomes]
rs6769236	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769261	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782181	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6782449	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784989	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789235	0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6790398	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802211	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs730158	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731632	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751357	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7615658	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626388	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7626424	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637666	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639809	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639850	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642400	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9289559	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940233	0.86[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825697	0.83[EUR][1000 genomes]
rs9834911	0.82[ASN][1000 genomes]
rs9845672	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846198	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846223	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854465	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9855722	0.95[EUR][1000 genomes];0.95[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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
2	chr3:138071200-138096600	Weak transcription	Aorta	Aorta
3	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:138078600-138100600	Weak transcription	NH-A	brain
5	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:138086200-138100400	Weak transcription	HepG2	liver
10	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:138087200-138097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:138087200-138100000	Weak transcription	Pancreas	Pancrea
13	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:138087400-138097000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:138089200-138100000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
17	chr3:138089400-138100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:138089400-138100000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
20	chr3:138089600-138097600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:138089600-138100200	Weak transcription	Lung	lung
22	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:138091000-138098000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:138091200-138100400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:138091400-138096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:138091400-138100800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:138091600-138098600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:138091800-138098000	Strong transcription	HSMM	muscle
29	chr3:138092200-138096800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:138093400-138097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:138093600-138100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:138093800-138100000	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:138093800-138100400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:138094000-138097000	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:138094200-138096800	Weak transcription	Osteobl	bone
37	chr3:138094400-138097200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:138094400-138100200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:138094600-138097400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:138094600-138099000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:138094600-138100600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:138094800-138100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:138095000-138096600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:138095000-138098000	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:138095200-138097600	Strong transcription	Brain Germinal Matrix	brain
46	chr3:138095400-138096600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:138095400-138097400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:138095600-138097400	Genic enhancers	Fetal Heart	heart
49	chr3:138095600-138098000	Strong transcription	Fetal Brain Female	brain
50	chr3:138095800-138096600	Weak transcription	Ovary	ovary

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