Variant report

Variant	rs2953295
Chromosome Location	chr4:120548222-120548223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120548059..120548579-chr4:120971160..120971673,2	K562	blood:
2	chr4:120235306..120236113-chr4:120548177..120548693,2	MCF-7	breast:
3	chr11:111666161..111667030-chr4:120547990..120548695,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10025536	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724055	0.81[EUR][1000 genomes]
rs11730798	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11731568	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103510	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13103899	0.80[EUR][1000 genomes]
rs13106925	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13109926	0.84[EUR][1000 genomes]
rs13116789	0.83[EUR][1000 genomes]
rs13118388	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13120581	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13121569	0.80[EUR][1000 genomes]
rs13124532	0.83[EUR][1000 genomes]
rs13133969	0.84[EUR][1000 genomes]
rs13136296	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13137511	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13140150	0.84[EUR][1000 genomes]
rs13147817	0.96[EUR][1000 genomes]
rs17292047	0.94[EUR][1000 genomes]
rs17358524	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17358860	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2389868	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389870	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2892870	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34601943	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34676199	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35289699	0.82[EUR][1000 genomes]
rs35581370	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35850447	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35967840	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35999787	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756155	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775846	0.91[EUR][1000 genomes]
rs3775850	0.82[EUR][1000 genomes]
rs3775851	0.82[EUR][1000 genomes]
rs3775856	0.84[EUR][1000 genomes]
rs4833620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4834782	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4834788	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834789	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834790	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61747388	0.80[EUR][1000 genomes]
rs62319606	0.94[EUR][1000 genomes]
rs62319609	0.84[EUR][1000 genomes]
rs62319612	0.95[EUR][1000 genomes]
rs62319647	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62319657	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62319658	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62321168	0.85[EUR][1000 genomes]
rs6817975	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7676589	0.91[EUR][1000 genomes];0.87[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
rs2953295	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs2953295	USP53	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120544400-120550600	Active TSS	Aorta	Aorta
2	chr4:120544800-120550800	Active TSS	Stomach Smooth Muscle	stomach
3	chr4:120545000-120549000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr4:120545200-120549000	Active TSS	Duodenum Mucosa	Duodenum
5	chr4:120545200-120550400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr4:120545200-120550600	Active TSS	Colon Smooth Muscle	Colon
7	chr4:120545600-120550600	Active TSS	Fetal Kidney	kidney
8	chr4:120545800-120550600	Active TSS	Rectal Smooth Muscle	rectum
9	chr4:120546000-120550600	Active TSS	Fetal Lung	lung
10	chr4:120546200-120550600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:120546400-120550400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:120546600-120550800	Active TSS	Right Atrium	heart
13	chr4:120546600-120551000	Active TSS	NHLF	lung
14	chr4:120546800-120548400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:120546800-120548600	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr4:120547000-120550400	Active TSS	Osteobl	bone
17	chr4:120547200-120550600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:120547400-120548400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:120547400-120549200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:120547400-120550200	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr4:120547400-120550200	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr4:120547400-120550600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:120547400-120550600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:120547400-120550800	Active TSS	H1 Cell Line	embryonic stem cell
25	chr4:120547400-120550800	Active TSS	NHDF-Ad	bronchial
26	chr4:120547600-120548400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:120547600-120549400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr4:120547600-120549800	Active TSS	Colonic Mucosa	Colon
29	chr4:120547600-120550200	Active TSS	Esophagus	oesophagus
30	chr4:120547600-120550400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:120547600-120550400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:120547600-120550400	Active TSS	Brain Anterior Caudate	brain
33	chr4:120547600-120550400	Active TSS	Pancreas	Pancrea
34	chr4:120547600-120550600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr4:120547600-120550600	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr4:120547600-120550600	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:120547600-120550600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:120547600-120550600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:120547600-120550600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:120547600-120550600	Active TSS	Left Ventricle	heart
41	chr4:120547600-120550600	Active TSS	Psoas Muscle	Psoas
42	chr4:120547600-120550600	Active TSS	Right Ventricle	heart
43	chr4:120547800-120548400	Flanking Bivalent TSS/Enh	Placenta	Placenta
44	chr4:120547800-120548400	Flanking Active TSS	NHEK	skin
45	chr4:120547800-120549000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:120547800-120549800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr4:120547800-120549800	Flanking Active TSS	HUVEC	blood vessel
48	chr4:120547800-120550400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr4:120547800-120550400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:120547800-120550400	Active TSS	Brain Angular Gyrus	brain

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