Variant report

Variant	rs253663
Chromosome Location	chr3:138096123-138096124
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: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1092338	0.80[ASN][1000 genomes]
rs1199329	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1199330	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1199332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1199337	1.00[CHB][hapmap]
rs1199338	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1199340	1.00[ASN][1000 genomes]
rs13324341	0.89[CHB][hapmap]
rs1678440	0.81[ASN][1000 genomes]
rs1678442	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1678443	1.00[CHB][hapmap];0.99[ASN][1000 genomes]
rs1720819	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1720823	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1720828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs181877	0.82[ASN][1000 genomes]
rs185244	0.81[ASN][1000 genomes]
rs1871398	1.00[EUR][1000 genomes]
rs253661	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs253665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs253667	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773757	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40593	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6789235	0.90[CHB][hapmap]
rs6807945	0.89[CHB][hapmap]
rs72630192	1.00[EUR][1000 genomes]
rs774009	1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs774013	0.86[EUR][1000 genomes]
rs796493	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

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	chr3:138080200-138096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:138085800-138096200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:138086200-138100400	Weak transcription	HepG2	liver
12	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:138087200-138097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:138087200-138100000	Weak transcription	Pancreas	Pancrea
15	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:138087400-138097000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:138089200-138096200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:138089200-138100000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
20	chr3:138089400-138100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:138089400-138100000	Weak transcription	Brain Angular Gyrus	brain
22	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
23	chr3:138089600-138097600	Weak transcription	Brain Substantia Nigra	brain
24	chr3:138089600-138100200	Weak transcription	Lung	lung
25	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:138091000-138098000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:138091200-138096400	Weak transcription	Brain Anterior Caudate	brain
28	chr3:138091200-138100400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:138091400-138096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:138091400-138100800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:138091600-138098600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:138091800-138098000	Strong transcription	HSMM	muscle
33	chr3:138092000-138096400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:138092200-138096800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:138093400-138097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:138093600-138100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:138093800-138100000	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:138093800-138100400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:138094000-138097000	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:138094200-138096800	Weak transcription	Osteobl	bone
42	chr3:138094400-138097200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:138094400-138100200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:138094600-138097400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:138094600-138099000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:138094600-138100600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:138094800-138096200	Weak transcription	Right Atrium	heart
48	chr3:138094800-138100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:138095000-138096600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:138095000-138098000	Strong transcription	Fetal Muscle Leg	muscle

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