Variant report

Variant	rs12503853
Chromosome Location	chr4:120503163-120503164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10012485	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021460	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10022664	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10518335	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12502511	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12642735	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12646525	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648259	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115778	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987179	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248236	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389863	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389864	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389866	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389869	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622499	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622500	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382361	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28412979	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540362	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564258	0.82[EUR][1000 genomes]
rs28566610	0.84[EUR][1000 genomes]
rs28610991	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28625289	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28650385	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2892867	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928993	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928994	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3733526	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3756154	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756157	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4337718	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4597811	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4604044	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4626181	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833622	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4834784	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534146	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6534147	0.80[EUR][1000 genomes]
rs6822275	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834347	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842674	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847164	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7659250	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670921	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7672961	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7681796	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7684899	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9998919	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12503853	RP11-33B1.1	cis	Thyroid	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120485800-120503800	Weak transcription	Aorta	Aorta
2	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
3	chr4:120486200-120503800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:120486200-120504800	Weak transcription	NH-A	brain
5	chr4:120486600-120516600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:120486800-120503600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:120486800-120515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:120486800-120516400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:120488200-120510200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:120488400-120504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:120492200-120513800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:120501000-120507000	Strong transcription	Osteobl	bone
15	chr4:120501200-120503800	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:120501800-120503200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:120501800-120505000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:120501800-120506800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:120501800-120520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:120502000-120506200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:120502000-120512400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:120502000-120516200	Weak transcription	Fetal Intestine Large	intestine
23	chr4:120502200-120507800	Strong transcription	NHLF	lung
24	chr4:120502200-120516400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
26	chr4:120502400-120503800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
28	chr4:120502600-120509000	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
30	chr4:120502800-120503200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:120503000-120503600	Weak transcription	Fetal Lung	lung
32	chr4:120503000-120503800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:120503000-120510000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr4:120503000-120517600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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