Variant report

Variant	rs1987179
Chromosome Location	chr4:120519934-120519935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10012485	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10021460	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10022664	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10518335	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724055	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs12502511	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12503853	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12642735	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12646525	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648259	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13103899	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs13115778	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13121569	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs13124532	0.81[TSI][hapmap]
rs17292047	0.81[TSI][hapmap]
rs17358524	0.81[TSI][hapmap]
rs17358860	0.89[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs2248236	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389863	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389864	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389866	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389869	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389870	0.89[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs2622499	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622500	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28382361	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28412979	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28540362	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28564258	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28566610	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28610991	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28625289	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28650385	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2892867	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928993	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928994	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3733526	0.92[CHD][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756154	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756157	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3775850	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs3775851	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs3775856	0.82[JPT][hapmap]
rs4337718	0.93[EUR][1000 genomes]
rs4597811	0.84[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4604044	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4626181	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4833622	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4834784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534146	0.92[CHD][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6534147	0.82[EUR][1000 genomes]
rs6822275	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834347	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6842674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847164	0.84[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7659250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7670921	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672961	0.91[CHD][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7681796	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7684899	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9998919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1987179	USP53	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
2	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:120501800-120520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
6	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
7	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
8	chr4:120504400-120520200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
10	chr4:120509600-120520000	Weak transcription	Psoas Muscle	Psoas
11	chr4:120511400-120520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:120512600-120530400	Weak transcription	Colonic Mucosa	Colon
13	chr4:120512800-120531600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:120514200-120520000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:120514200-120528600	Weak transcription	Gastric	stomach
16	chr4:120516000-120520200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:120516000-120520200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:120516800-120527800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:120517000-120520200	Weak transcription	Fetal Intestine Large	intestine
20	chr4:120517000-120527600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:120517000-120527800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:120517000-120531400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:120517000-120536600	Weak transcription	Ovary	ovary
24	chr4:120518000-120520200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr4:120518800-120520000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:120518800-120524400	Weak transcription	Fetal Heart	heart
27	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:120519000-120533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:120519400-120520000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:120519400-120521200	ZNF genes & repeats	Fetal Lung	lung
31	chr4:120519600-120520000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:120519600-120520200	Enhancers	Rectal Smooth Muscle	rectum
33	chr4:120519600-120520400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr4:120519600-120528600	Strong transcription	Osteobl	bone
35	chr4:120519800-120520000	Genic enhancers	Colon Smooth Muscle	Colon
36	chr4:120519800-120520000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:120519800-120520200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:120519800-120520200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr4:120519800-120520200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr4:120519800-120520200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
41	chr4:120519800-120520400	ZNF genes & repeats	Aorta	Aorta
42	chr4:120519800-120520400	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr4:120519800-120520600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr4:120519800-120520600	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr4:120519800-120520800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:120519800-120521000	ZNF genes & repeats	NHLF	lung
47	chr4:120519800-120527600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:120519800-120527800	Weak transcription	H1 Cell Line	embryonic stem cell

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