Variant report

Variant	rs28540362
Chromosome Location	chr4:120491877-120491878
allele	A/G
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:48)

rs_ID	r²[population]
rs10012485	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021460	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10022664	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10518335	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12502511	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12503853	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642735	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12646525	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648259	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115778	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987179	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248236	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389863	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389864	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389866	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389869	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622499	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622500	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382361	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28412979	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564258	0.81[EUR][1000 genomes]
rs28566610	0.84[EUR][1000 genomes]
rs28610991	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28625289	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28650385	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2892867	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928993	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928994	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3733526	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3756154	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756157	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4337718	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4597811	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4604044	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4626181	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833622	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4834784	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534146	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6822275	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834347	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842674	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847164	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7659250	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670921	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7672961	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7681796	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7684899	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9998919	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
rs28540362	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs28540362	RP11-33B1.1	cis	Thyroid	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
2	chr4:120478600-120501000	Weak transcription	Fetal Stomach	stomach
3	chr4:120485000-120493000	Weak transcription	Left Ventricle	heart
4	chr4:120485600-120494600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:120485800-120503800	Weak transcription	Aorta	Aorta
6	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
7	chr4:120486200-120503800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:120486200-120504800	Weak transcription	NH-A	brain
9	chr4:120486600-120502800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:120486600-120516600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:120486800-120503600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:120486800-120515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:120486800-120516400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:120488000-120501000	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:120488200-120492200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:120488200-120501200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:120488200-120510200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:120488400-120504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:120489200-120492400	Enhancers	Colon Smooth Muscle	Colon
21	chr4:120490200-120492800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:120490800-120492000	Enhancers	Stomach Smooth Muscle	stomach
23	chr4:120490800-120492200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:120490800-120493200	Enhancers	NHDF-Ad	bronchial
25	chr4:120490800-120493400	Enhancers	Osteobl	bone
26	chr4:120491000-120492200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:120491000-120492400	Enhancers	Fetal Lung	lung
28	chr4:120491200-120492000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:120491200-120492000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr4:120491200-120492200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:120491200-120492400	Enhancers	Rectal Smooth Muscle	rectum
32	chr4:120491400-120492000	Enhancers	Ovary	ovary
33	chr4:120491600-120492000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:120491600-120493400	Genic enhancers	NHLF	lung
35	chr4:120491800-120492400	Enhancers	Right Atrium	heart
36	chr4:120491800-120492400	Enhancers	HSMMtube	muscle
37	chr4:120491800-120494400	Weak transcription	Fetal Kidney	kidney

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