Variant report

Variant	rs2389870
Chromosome Location	chr4:120522038-120522039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10012485	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs10025536	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10518335	0.84[CEU][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap]
rs11724055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730798	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11731568	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12646525	0.89[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs13103510	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13103899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13106925	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13107334	0.81[GIH][hapmap];0.84[TSI][hapmap]
rs13116789	1.00[CHB][hapmap]
rs13118388	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13120581	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13121569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13124532	0.87[TSI][hapmap]
rs13133969	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13136296	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13137511	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13140150	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13147817	0.82[EUR][1000 genomes]
rs17292047	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17358524	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17358860	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987179	0.89[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs2248236	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs2389863	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs2389866	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs2389868	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2389869	0.89[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs2622499	0.89[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs2892870	0.82[EUR][1000 genomes]
rs2953295	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34601943	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34676199	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35264119	0.82[EUR][1000 genomes]
rs35289699	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35581370	0.81[EUR][1000 genomes]
rs35850447	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35967840	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35999787	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756154	0.89[CEU][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap]
rs3756155	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775846	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs3775850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775851	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3775856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833620	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4834782	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4834788	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4834789	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4834790	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61747388	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62319574	0.80[EUR][1000 genomes]
rs62319578	0.82[EUR][1000 genomes]
rs62319606	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62319609	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62319612	0.85[EUR][1000 genomes]
rs62319647	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62319657	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62319658	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6817975	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6822275	0.83[EUR][1000 genomes]
rs71614451	0.82[EUR][1000 genomes]
rs7676589	0.80[EUR][1000 genomes]
rs7684899	0.88[CEU][hapmap];0.89[JPT][hapmap]

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
rs2389870	USP53	cis	parietal	SCAN
rs2389870	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
4	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
5	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
6	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
7	chr4:120512600-120530400	Weak transcription	Colonic Mucosa	Colon
8	chr4:120512800-120531600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:120514200-120528600	Weak transcription	Gastric	stomach
10	chr4:120516800-120527800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:120517000-120527600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:120517000-120527800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:120517000-120531400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:120517000-120536600	Weak transcription	Ovary	ovary
15	chr4:120518800-120524400	Weak transcription	Fetal Heart	heart
16	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:120519000-120533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:120519600-120528600	Strong transcription	Osteobl	bone
19	chr4:120519800-120527600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:120519800-120527800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:120520000-120522200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:120520200-120524000	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:120520200-120525000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:120520200-120525200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:120520200-120525200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:120520200-120525200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:120520200-120527800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:120520200-120527800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:120520200-120529800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:120520200-120536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:120520400-120522200	Weak transcription	Aorta	Aorta
32	chr4:120520400-120525400	Weak transcription	Small Intestine	intestine
33	chr4:120520400-120525800	Weak transcription	Psoas Muscle	Psoas
34	chr4:120520400-120533200	Weak transcription	Fetal Intestine Small	intestine
35	chr4:120520400-120537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:120520600-120524400	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:120520600-120527800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:120520600-120529600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:120520800-120527600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:120520800-120527800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:120520800-120529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:120521000-120524000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:120521000-120524600	Strong transcription	NHLF	lung
44	chr4:120521000-120529800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
46	chr4:120521200-120527400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:120521400-120527800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:120521600-120524600	Strong transcription	Fetal Lung	lung
49	chr4:120522000-120530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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