Variant report

Variant	rs35999787
Chromosome Location	chr4:120519104-120519105
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10025536	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724055	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11730798	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11731568	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13103510	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103899	0.82[EUR][1000 genomes]
rs13106925	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13109926	0.84[EUR][1000 genomes]
rs13116789	0.85[EUR][1000 genomes]
rs13118388	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13120581	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13121569	0.82[EUR][1000 genomes]
rs13124532	0.85[EUR][1000 genomes]
rs13133969	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13136296	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13137511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13140150	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13147817	0.94[EUR][1000 genomes]
rs17292047	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17358524	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17358860	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2389868	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389870	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2892870	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2953295	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34601943	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34676199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35289699	0.84[EUR][1000 genomes]
rs35581370	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35850447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35967840	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756155	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775846	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3775850	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775851	0.84[EUR][1000 genomes]
rs3775856	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4833620	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4834782	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834788	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4834789	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4834790	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61747388	0.82[EUR][1000 genomes]
rs62319606	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62319609	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62319612	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62319647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319657	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62319658	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62321168	0.85[EUR][1000 genomes]
rs6817975	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7676589	0.91[EUR][1000 genomes];0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35999787	USP53	cis	Whole Blood	GTEx
rs35999787	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

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	chr4:120504600-120519800	Weak transcription	Fetal Intestine Small	intestine
10	chr4:120505000-120519800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:120505600-120519800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
13	chr4:120509600-120520000	Weak transcription	Psoas Muscle	Psoas
14	chr4:120511400-120520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:120511600-120519600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:120512600-120519600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:120512600-120530400	Weak transcription	Colonic Mucosa	Colon
18	chr4:120512800-120531600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:120514200-120520000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:120514200-120528600	Weak transcription	Gastric	stomach
21	chr4:120514800-120519400	Weak transcription	Fetal Lung	lung
22	chr4:120515000-120519800	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:120516000-120519800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:120516000-120520200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:120516000-120520200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr4:120516800-120527800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:120517000-120519400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:120517000-120519800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:120517000-120519800	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:120517000-120520200	Weak transcription	Fetal Intestine Large	intestine
31	chr4:120517000-120527600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:120517000-120527800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:120517000-120531400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:120517000-120536600	Weak transcription	Ovary	ovary
35	chr4:120517200-120519600	Weak transcription	Osteobl	bone
36	chr4:120517400-120519800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:120517600-120519600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:120517800-120519400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:120518000-120520200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr4:120518200-120519400	Weak transcription	NHLF	lung
41	chr4:120518400-120519800	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr4:120518800-120519600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:120518800-120519800	Weak transcription	Aorta	Aorta
44	chr4:120518800-120519800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:120518800-120520000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:120518800-120524400	Weak transcription	Fetal Heart	heart
47	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:120519000-120533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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