Variant report

Variant	rs2389863
Chromosome Location	chr4:120507664-120507665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10012485	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10021460	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10022664	0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10518335	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11724055	0.84[CEU][hapmap]
rs12502511	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12503853	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12642735	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12646525	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12648259	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13103899	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs13115778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13121569	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs13124532	0.81[TSI][hapmap]
rs17292047	0.81[TSI][hapmap]
rs17358524	0.81[TSI][hapmap]
rs17358860	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs1987179	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]
rs2248236	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389864	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389866	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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]
rs2389869	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[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];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389870	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs2622499	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622500	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28382361	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28412979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28540362	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28564258	0.83[EUR][1000 genomes]
rs28566610	0.86[EUR][1000 genomes]
rs28610991	0.84[EUR][1000 genomes]
rs28625289	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28650385	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2892867	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2928993	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2928994	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3733526	0.85[CHB][hapmap];0.85[CHD][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3756154	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756157	0.85[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3775850	0.84[CEU][hapmap]
rs3775851	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs4337718	0.92[EUR][1000 genomes]
rs4597811	0.85[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4604044	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4626181	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4833622	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4834784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6534146	0.85[CHB][hapmap];0.85[CHD][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6534147	0.81[EUR][1000 genomes]
rs6822275	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6834347	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6842674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847164	0.85[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7659250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7670921	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7672961	0.85[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7681796	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7684899	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9998919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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
rs2389863	RP11-33B1.1	cis	Thyroid	GTEx
rs2389863	USP53	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
2	chr4:120486600-120516600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:120486800-120515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:120486800-120516400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:120488200-120510200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:120492200-120513800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:120501800-120520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:120502000-120512400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:120502000-120516200	Weak transcription	Fetal Intestine Large	intestine
12	chr4:120502200-120507800	Strong transcription	NHLF	lung
13	chr4:120502200-120516400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
15	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
16	chr4:120502600-120509000	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
18	chr4:120503000-120510000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:120503000-120517600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:120503200-120516400	Weak transcription	Ovary	ovary
21	chr4:120503200-120517800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:120504400-120516400	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:120504400-120520200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:120504600-120519800	Weak transcription	Fetal Intestine Small	intestine
25	chr4:120505000-120519800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:120505200-120518400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:120505400-120511000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:120505400-120514400	Weak transcription	NH-A	brain
29	chr4:120505400-120516600	Weak transcription	Aorta	Aorta
30	chr4:120505600-120519800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:120506000-120509800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:120506000-120514000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:120506000-120514000	Weak transcription	Fetal Lung	lung
34	chr4:120506000-120515400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:120506000-120516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
37	chr4:120507000-120512800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:120507400-120509000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:120507400-120512400	Weak transcription	Osteobl	bone

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