Variant report

Variant	rs13240650
Chromosome Location	chr7:48131546-48131547
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	chr7:48128689..48131153-chr7:48131226..48133019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183696	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10278152	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768083	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554494	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581415	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1581416	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686796	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686800	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686802	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686803	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708866	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708867	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708868	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708869	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708870	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708871	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3752889	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752890	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763504	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763505	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59688958	0.83[ASN][1000 genomes]
rs62447120	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6968763	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7458962	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7459020	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793905	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794100	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804178	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9639019	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639991	0.85[EUR][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv997355	chr7:48128431-48138826	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13240650	UPP1	cis	Muscle Skeletal	GTEx
rs13240650	UPP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48129000-48137000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:48129600-48131600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
3	chr7:48129600-48134600	Weak transcription	Aorta	Aorta
4	chr7:48129600-48136200	Transcr. at gene 5' and 3'	NHEK	skin
5	chr7:48129600-48141000	Weak transcription	Gastric	stomach
6	chr7:48129600-48141200	Weak transcription	Ovary	ovary
7	chr7:48129800-48131600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr7:48130000-48131800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:48130000-48132000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr7:48130000-48132000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:48130000-48132200	Transcr. at gene 5' and 3'	HMEC	breast
12	chr7:48130000-48134000	Weak transcription	HSMMtube	muscle
13	chr7:48130000-48135600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:48130200-48131600	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:48130200-48131600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
16	chr7:48130200-48131600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr7:48130200-48131600	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:48130200-48131800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr7:48130200-48132600	Weak transcription	Right Ventricle	heart
20	chr7:48130200-48132800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:48130200-48133000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:48130200-48133200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:48130200-48133200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr7:48130200-48134000	Weak transcription	Brain Angular Gyrus	brain
25	chr7:48130200-48134000	Weak transcription	HSMM	muscle
26	chr7:48130200-48134200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:48130200-48134200	Weak transcription	Stomach Mucosa	stomach
28	chr7:48130200-48134600	Weak transcription	Fetal Heart	heart
29	chr7:48130200-48135600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:48130200-48138200	Weak transcription	Pancreas	Pancrea
31	chr7:48130200-48141400	Weak transcription	Brain Substantia Nigra	brain
32	chr7:48130200-48146800	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:48130200-48148200	Weak transcription	Right Atrium	heart
34	chr7:48130400-48131600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:48130400-48131600	Weak transcription	Esophagus	oesophagus
36	chr7:48130400-48131600	Weak transcription	Fetal Intestine Large	intestine
37	chr7:48130400-48131800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr7:48130400-48132200	Genic enhancers	Primary monocytes fromperipheralblood	blood
39	chr7:48130400-48132200	Enhancers	Osteobl	bone
40	chr7:48130400-48132600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr7:48130400-48133000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr7:48130400-48133000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:48130400-48134000	Weak transcription	GM12878-XiMat	blood
44	chr7:48130400-48134000	Weak transcription	NHLF	lung
45	chr7:48130400-48135200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:48130400-48135600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:48130400-48136000	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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