Variant report

Variant	rs4742952
Chromosome Location	chr9:108323151-108323152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1018847	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491808	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115847	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17250623	0.88[EUR][1000 genomes]
rs17251166	0.86[EUR][1000 genomes]
rs17308339	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17309137	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17309319	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17309806	0.91[EUR][1000 genomes]
rs2068267	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2771028	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2771037	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2771039	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2771044	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2771045	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2812298	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812299	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812300	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812301	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812302	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812304	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812306	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812309	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2812311	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2812312	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34787999	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41277785	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742649	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742651	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742653	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742654	0.85[EUR][1000 genomes]
rs4742946	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4742949	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742950	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742953	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742954	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742955	0.89[EUR][1000 genomes]
rs4742956	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57432946	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57597571	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59474306	0.87[EUR][1000 genomes]
rs60126815	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62575093	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62575095	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62575101	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62575102	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62575104	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575105	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575106	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575112	0.86[EUR][1000 genomes]
rs62575114	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575144	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62575145	0.91[EUR][1000 genomes]
rs7024265	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035783	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7037972	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851777	0.88[EUR][1000 genomes]
rs7872377	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9408799	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9409062	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4742952	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321000-108324400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:108321000-108324400	Weak transcription	Esophagus	oesophagus
3	chr9:108321200-108323200	Weak transcription	Ovary	ovary
4	chr9:108321200-108325600	Weak transcription	Left Ventricle	heart
5	chr9:108321200-108335600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:108321400-108323400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:108321400-108323800	Weak transcription	Fetal Heart	heart
8	chr9:108321400-108324000	Weak transcription	Primary B cells from cord blood	blood
9	chr9:108321400-108324400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:108321400-108324600	Weak transcription	Fetal Kidney	kidney
11	chr9:108321400-108325000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:108321600-108323400	Weak transcription	Primary T cells from cord blood	blood
13	chr9:108321600-108323400	Weak transcription	Liver	Liver
14	chr9:108321600-108323800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:108321600-108323800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:108321600-108323800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:108321600-108323800	Weak transcription	Fetal Lung	lung
18	chr9:108321600-108324000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:108321600-108324000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:108321600-108324000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:108321600-108324200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:108321600-108324200	Weak transcription	A549	lung
23	chr9:108321600-108324400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr9:108321600-108324400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr9:108321600-108324400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:108321600-108324400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:108321600-108324400	Weak transcription	Fetal Brain Male	brain
28	chr9:108321600-108324400	Weak transcription	NHEK	skin
29	chr9:108321600-108324400	Weak transcription	NHLF	lung
30	chr9:108321600-108325000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:108321600-108325000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:108321600-108325200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr9:108321600-108325600	Weak transcription	Thymus	Thymus
34	chr9:108321600-108326000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr9:108321600-108326200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:108321600-108336000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:108321600-108336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:108321600-108336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:108321600-108338000	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:108321600-108353600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:108321600-108354000	Weak transcription	Right Ventricle	heart
42	chr9:108321600-108360200	Weak transcription	HSMM	muscle
43	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:108321800-108324400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr9:108321800-108324400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:108322000-108325400	ZNF genes & repeats	Fetal Brain Female	brain
47	chr9:108322200-108323400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr9:108322200-108323800	Weak transcription	GM12878-XiMat	blood
49	chr9:108322200-108334600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:108322600-108324200	Weak transcription	Dnd41	blood

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