Variant report

Variant	rs73415720
Chromosome Location	chr12:121344515-121344516
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	chr12:121336041..121337901-chr12:121343531..121346196,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10774572	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10849807	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065300	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065307	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065311	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11065324	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065332	0.92[ASN][1000 genomes]
rs1151849	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1151859	0.88[ASN][1000 genomes]
rs1151862	0.88[ASN][1000 genomes]
rs1168944	0.88[ASN][1000 genomes]
rs1168946	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1168948	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1168953	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1177585	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1179939	0.88[ASN][1000 genomes]
rs12371178	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12372231	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12580949	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12809299	0.80[EUR][1000 genomes]
rs12822123	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12831094	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1542859	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1696357	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1696390	0.95[ASN][1000 genomes]
rs1718188	0.98[ASN][1000 genomes]
rs2393716	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2650017	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2701177	0.98[ASN][1000 genomes]
rs2701184	0.99[ASN][1000 genomes]
rs34009825	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35905305	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809313	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3897746	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4454799	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4766980	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4767941	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs487943	0.84[ASN][1000 genomes]
rs520753	0.85[ASN][1000 genomes]
rs533264	0.85[ASN][1000 genomes]
rs548452	0.83[ASN][1000 genomes]
rs58918988	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs602984	0.84[ASN][1000 genomes]
rs609700	0.85[ASN][1000 genomes]
rs610694	0.85[ASN][1000 genomes]
rs61946382	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61946383	0.96[ASN][1000 genomes]
rs61946384	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61946385	0.96[ASN][1000 genomes]
rs61946386	0.96[ASN][1000 genomes]
rs647881	0.85[ASN][1000 genomes]
rs665585	0.83[ASN][1000 genomes]
rs666976	0.81[ASN][1000 genomes]
rs73413868	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73415734	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967190	0.92[ASN][1000 genomes]
rs7969140	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7980311	0.99[ASN][1000 genomes]
rs869781	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs904628	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv560448	chr12:121341477-121364324	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv560452	chr12:121341581-121357934	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv560453	chr12:121342186-121364324	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73415720	ACADS	cis	Thyroid	GTEx
rs73415720	SPPL3	cis	Nerve Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121342400-121345000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:121342600-121345000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:121342600-121345000	Weak transcription	Aorta	Aorta
4	chr12:121342600-121345400	Weak transcription	Lung	lung
5	chr12:121342600-121345400	Weak transcription	Right Atrium	heart
6	chr12:121342600-121345800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:121342600-121345800	Enhancers	HMEC	breast
8	chr12:121342600-121346000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:121342600-121347600	Enhancers	Placenta	Placenta
10	chr12:121342800-121344800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:121342800-121344800	Weak transcription	Hela-S3	cervix
12	chr12:121342800-121345000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:121342800-121345000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:121342800-121345000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:121342800-121345000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:121342800-121345000	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:121342800-121345000	Weak transcription	HSMM	muscle
18	chr12:121342800-121345000	Weak transcription	NH-A	brain
19	chr12:121342800-121345000	Weak transcription	NHDF-Ad	bronchial
20	chr12:121342800-121345000	Enhancers	NHEK	skin
21	chr12:121342800-121345000	Weak transcription	Osteobl	bone
22	chr12:121342800-121345200	Weak transcription	NHLF	lung
23	chr12:121342800-121345800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:121342800-121346200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:121342800-121346600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:121342800-121347000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:121342800-121347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:121342800-121347400	Weak transcription	GM12878-XiMat	blood
29	chr12:121343000-121344800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:121343000-121344800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:121343000-121344800	Weak transcription	Fetal Heart	heart
32	chr12:121343000-121345000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:121343000-121362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:121343200-121347200	Weak transcription	Spleen	Spleen
35	chr12:121343600-121345800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr12:121343800-121345000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:121343800-121347400	Enhancers	Esophagus	oesophagus
38	chr12:121344000-121344800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:121344200-121344600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:121344400-121345000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:121344400-121345000	Active TSS	HepG2	liver
42	chr12:121344400-121345400	Weak transcription	Psoas Muscle	Psoas
43	chr12:121344400-121346000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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