Variant report

Variant	rs3752890
Chromosome Location	chr7:48129368-48129369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48017456..48020295-chr7:48126750..48129913,5	K562	blood:
2	chr7:48017568..48020341-chr7:48128356..48131105,2	MCF-7	breast:
3	chr7:48017535..48019169-chr7:48128413..48129998,2	K562	blood:
4	chr2:190648263..190649127-chr7:48128850..48129707,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000136273	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000064933	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10278152	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768083	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13227958	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13240650	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1554494	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1581415	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1581416	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2686796	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2686800	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2686802	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2686803	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708866	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708867	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708868	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708869	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708870	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708871	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3752889	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763504	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763505	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59688958	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62447120	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6968763	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7341420	0.81[AMR][1000 genomes]
rs7385009	0.81[AMR][1000 genomes]
rs7458962	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7459020	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7793905	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7794100	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804178	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9639019	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9639991	0.87[AMR][1000 genomes];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3752890	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48127200-48129600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:48127200-48129600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr7:48127600-48129600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:48127600-48129600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:48127600-48130000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:48127600-48130200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr7:48127600-48130200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr7:48127600-48130200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr7:48127600-48130400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:48127600-48130400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr7:48127600-48130400	Active TSS	Rectal Smooth Muscle	rectum
12	chr7:48127600-48130600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr7:48127800-48129400	Active TSS	HepG2	liver
14	chr7:48127800-48129600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:48127800-48129800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr7:48127800-48129800	Active TSS	Brain Anterior Caudate	brain
17	chr7:48127800-48130200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:48127800-48130200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:48127800-48130200	Active TSS	Colon Smooth Muscle	Colon
20	chr7:48127800-48130200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr7:48127800-48130400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr7:48127800-48130400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr7:48127800-48130600	Active TSS	Psoas Muscle	Psoas
24	chr7:48128000-48129400	Bivalent/Poised TSS	Fetal Brain Female	brain
25	chr7:48128000-48129400	Active TSS	Spleen	Spleen
26	chr7:48128000-48129600	Active TSS	Aorta	Aorta
27	chr7:48128000-48129600	Active TSS	Brain Angular Gyrus	brain
28	chr7:48128000-48129600	Active TSS	Duodenum Mucosa	Duodenum
29	chr7:48128000-48129600	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr7:48128000-48129800	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr7:48128000-48129800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:48128000-48129800	Active TSS	Lung	lung
33	chr7:48128000-48130000	Active TSS	Left Ventricle	heart
34	chr7:48128000-48130000	Active TSS	A549	lung
35	chr7:48128000-48130000	Active TSS	HSMMtube	muscle
36	chr7:48128000-48130200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr7:48128000-48130200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:48128000-48130200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:48128000-48130200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr7:48128000-48130200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:48128000-48130400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:48128000-48130600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:48128000-48131200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr7:48128200-48129400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr7:48128200-48129400	Active TSS	Fetal Heart	heart
46	chr7:48128200-48129400	Active TSS	Gastric	stomach
47	chr7:48128200-48129400	Active TSS	Hela-S3	cervix
48	chr7:48128200-48129600	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr7:48128200-48129600	Active TSS	Fetal Intestine Small	intestine
50	chr7:48128200-48129600	Active TSS	Ovary	ovary

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