Variant report

Variant	rs1553604
Chromosome Location	chr11:93582153-93582154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93574931..93577812-chr11:93581289..93582861,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10765637	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10831106	0.80[EUR][1000 genomes]
rs11020572	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1605288	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1605289	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1605291	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1848076	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1848078	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1848079	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1973546	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3913857	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4753506	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4753507	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4753510	0.80[EUR][1000 genomes]
rs4753511	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4753512	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs584462	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs589024	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs608479	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs622372	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6483267	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7108328	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7111123	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7111771	0.93[ASW][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7112538	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7122140	0.81[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs7127486	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7130590	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7130837	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs732358	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs732359	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7940081	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7947606	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1553604	GPR83	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93572600-93582800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:93574400-93582800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr11:93575800-93582600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:93575800-93582800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:93576600-93583000	Weak transcription	Esophagus	oesophagus
6	chr11:93578400-93583800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:93579000-93582600	Weak transcription	NHDF-Ad	bronchial
8	chr11:93579000-93582800	Weak transcription	Placenta	Placenta
9	chr11:93579000-93583200	Weak transcription	HMEC	breast
10	chr11:93579200-93582800	Weak transcription	Osteobl	bone
11	chr11:93579600-93583000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:93579600-93583000	Weak transcription	NHEK	skin
13	chr11:93579800-93582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:93579800-93582800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:93579800-93582800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:93579800-93582800	Weak transcription	NH-A	brain
17	chr11:93579800-93583000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:93579800-93583000	Weak transcription	NHLF	lung
19	chr11:93579800-93583200	Weak transcription	HSMM	muscle
20	chr11:93580000-93583000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:93580600-93582600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:93580600-93582800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:93581000-93582800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:93581000-93582800	Enhancers	Stomach Mucosa	stomach
25	chr11:93581600-93583000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:93581800-93582600	Enhancers	Duodenum Mucosa	Duodenum
27	chr11:93581800-93582800	Enhancers	Fetal Intestine Large	intestine
28	chr11:93581800-93582800	Enhancers	Fetal Intestine Small	intestine
29	chr11:93581800-93582800	Enhancers	Rectal Mucosa Donor 31	rectum

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