Variant report

Variant	rs10253220
Chromosome Location	chr7:48075477-48075478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10225968	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10247913	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253238	0.85[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs10256256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10261930	0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10951937	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs10951938	0.87[CEU][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs10951940	0.96[EUR][1000 genomes]
rs10951941	0.93[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs10951942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11761275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11762077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764799	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11766144	0.96[EUR][1000 genomes]
rs11766891	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11767002	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs11768277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11772387	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11772633	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11773348	0.85[EUR][1000 genomes]
rs12535580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12702405	0.80[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs12702406	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1318327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230023	0.85[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1574242	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs1915960	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1915962	0.92[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs1915965	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1915966	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915967	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915968	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140113	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2348666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2348667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2348669	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2348670	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2881991	0.88[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2881992	0.85[EUR][1000 genomes]
rs4332046	0.95[EUR][1000 genomes]
rs4354227	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4618593	0.89[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs6978838	1.00[CEU][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6979699	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7357251	0.93[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7357327	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7456745	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779252	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7789930	0.90[YRI][hapmap]
rs7791084	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7791572	0.88[CEU][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs7791823	0.93[EUR][1000 genomes]
rs7800590	0.86[AMR][1000 genomes]
rs7807611	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7807612	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7807654	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7807750	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7808462	0.93[EUR][1000 genomes]
rs9690905	0.92[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][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	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	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10253220	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48074600-48076000	Bivalent/Poised TSS	HSMMtube	muscle
2	chr7:48074800-48075600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:48074800-48075600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:48074800-48075800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr7:48074800-48076000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
6	chr7:48074800-48076000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr7:48074800-48076000	Flanking Active TSS	Ovary	ovary
8	chr7:48074800-48076200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr7:48074800-48076200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:48075000-48075600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:48075000-48075600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
12	chr7:48075000-48075800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr7:48075000-48075800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
14	chr7:48075000-48075800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
15	chr7:48075000-48075800	Active TSS	Aorta	Aorta
16	chr7:48075000-48075800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
17	chr7:48075000-48075800	Flanking Active TSS	Gastric	stomach
18	chr7:48075000-48076000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:48075000-48076000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
20	chr7:48075000-48076000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr7:48075000-48076000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr7:48075000-48076000	Flanking Active TSS	Right Ventricle	heart
23	chr7:48075000-48076000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
24	chr7:48075000-48076000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
25	chr7:48075000-48076200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr7:48075000-48076200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:48075000-48076400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr7:48075000-48076400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr7:48075200-48075600	Bivalent Enhancer	Small Intestine	intestine
30	chr7:48075200-48075600	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
31	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
32	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	Liver	Liver
33	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
34	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
35	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
36	chr7:48075200-48075800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
37	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
38	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
39	chr7:48075200-48075800	Flanking Bivalent TSS/Enh	HSMM	muscle
40	chr7:48075200-48076000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
43	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
44	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
45	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
47	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:48075200-48076000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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