Variant report

Variant	rs9639019
Chromosome Location	chr7:48132391-48132392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48128828..48131724-chr7:48131867..48135623,4	K562	blood:
2	chr7:48128689..48131153-chr7:48131226..48133019,2	MCF-7	breast:
3	chr7:48127323..48129947-chr7:48131574..48136086,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183696	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10278152	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11768083	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227958	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13240650	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1554494	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1581415	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1581416	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686796	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2686800	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686802	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686803	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708866	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708867	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708868	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708869	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708870	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708871	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3752889	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3752890	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763504	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3763505	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59688958	0.82[ASN][1000 genomes]
rs62447120	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6968763	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7458962	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7459020	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793905	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794100	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804178	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9639991	0.86[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9639019	UPP1	cis	Thyroid	GTEx
rs9639019	UPP1	cis	Esophagus Muscularis	GTEx
rs9639019	UPP1	cis	Muscle Skeletal	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	chr7:48129600-48134600	Weak transcription	Aorta	Aorta
3	chr7:48129600-48136200	Transcr. at gene 5' and 3'	NHEK	skin
4	chr7:48129600-48141000	Weak transcription	Gastric	stomach
5	chr7:48129600-48141200	Weak transcription	Ovary	ovary
6	chr7:48130000-48134000	Weak transcription	HSMMtube	muscle
7	chr7:48130000-48135600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:48130200-48132600	Weak transcription	Right Ventricle	heart
9	chr7:48130200-48132800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:48130200-48133000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:48130200-48133200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:48130200-48133200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr7:48130200-48134000	Weak transcription	Brain Angular Gyrus	brain
14	chr7:48130200-48134000	Weak transcription	HSMM	muscle
15	chr7:48130200-48134200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:48130200-48134200	Weak transcription	Stomach Mucosa	stomach
17	chr7:48130200-48134600	Weak transcription	Fetal Heart	heart
18	chr7:48130200-48135600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:48130200-48138200	Weak transcription	Pancreas	Pancrea
20	chr7:48130200-48141400	Weak transcription	Brain Substantia Nigra	brain
21	chr7:48130200-48146800	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:48130200-48148200	Weak transcription	Right Atrium	heart
23	chr7:48130400-48132600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:48130400-48133000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:48130400-48133000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:48130400-48134000	Weak transcription	GM12878-XiMat	blood
27	chr7:48130400-48134000	Weak transcription	NHLF	lung
28	chr7:48130400-48135200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:48130400-48135600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:48130400-48136000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr7:48130400-48136000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr7:48130400-48136200	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr7:48130400-48137000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:48130400-48141400	Weak transcription	HepG2	liver
38	chr7:48130400-48149800	Weak transcription	Fetal Kidney	kidney
39	chr7:48130400-48150000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr7:48130600-48132600	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr7:48130600-48139200	Genic enhancers	Placenta	Placenta
42	chr7:48130600-48143600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:48130800-48135600	Strong transcription	Liver	Liver
44	chr7:48130800-48149200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:48131000-48132400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:48131000-48132800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr7:48131000-48135000	Strong transcription	Left Ventricle	heart
48	chr7:48131000-48135200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:48131000-48135200	Strong transcription	Colonic Mucosa	Colon
50	chr7:48131000-48135200	Strong transcription	Stomach Smooth Muscle	stomach

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