Variant report

Variant	rs2812300
Chromosome Location	chr9:108207945-108207946
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:108207684-108208189	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:108206685..108208191-chr9:108209872..108211724,2	K562	blood:
2	chr9:108196491..108199020-chr9:108207109..108209245,2	K562	blood:
3	chr9:108207677..108209988-chr9:108545420..108547936,2	K562	blood:

Variant related genes	Relation type
FSD1L	TF binding region
ENSG00000106701	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1018847	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10491808	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12115847	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17250623	0.81[EUR][1000 genomes]
rs17308339	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17309137	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17309319	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17309806	0.84[EUR][1000 genomes]
rs2068267	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2771028	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2771037	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2771039	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2771044	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2771045	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2812298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2812299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812301	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812302	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812306	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2812309	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812311	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2812312	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34787999	0.84[EUR][1000 genomes]
rs41277785	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742649	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742651	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742653	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742946	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742949	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742950	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742952	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742953	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742954	0.85[EUR][1000 genomes]
rs4742955	0.82[EUR][1000 genomes]
rs4742956	0.84[EUR][1000 genomes]
rs57432946	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57597571	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60126815	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62575093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575095	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62575101	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62575102	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575104	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62575105	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62575106	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62575114	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62575144	0.83[EUR][1000 genomes]
rs62575145	0.84[EUR][1000 genomes]
rs7024265	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7035783	0.83[EUR][1000 genomes]
rs7037972	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7851777	0.81[EUR][1000 genomes]
rs7872377	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9408799	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409062	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2812300	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108195800-108209800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:108201000-108209600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr9:108201600-108209800	Weak transcription	NHLF	lung
4	chr9:108203400-108208400	Enhancers	Brain Substantia Nigra	brain
5	chr9:108204200-108209800	Weak transcription	Right Ventricle	heart
6	chr9:108204600-108209200	Weak transcription	Fetal Brain Male	brain
7	chr9:108204600-108209800	Weak transcription	Liver	Liver
8	chr9:108204600-108209800	Weak transcription	Fetal Heart	heart
9	chr9:108205600-108208400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:108206000-108209800	Weak transcription	Psoas Muscle	Psoas
11	chr9:108206200-108208200	Enhancers	HSMM	muscle
12	chr9:108206200-108209600	Enhancers	Fetal Muscle Leg	muscle
13	chr9:108206400-108208200	Enhancers	Brain Angular Gyrus	brain
14	chr9:108206600-108208000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:108206600-108208200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:108206600-108208200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:108206600-108208200	Enhancers	HSMMtube	muscle
18	chr9:108206600-108209600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:108206800-108209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:108206800-108209400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:108206800-108209600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:108207000-108209200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:108207000-108209400	Weak transcription	NHEK	skin
24	chr9:108207000-108209600	Weak transcription	HMEC	breast
25	chr9:108207000-108209600	Weak transcription	NH-A	brain
26	chr9:108207000-108209800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:108207200-108208200	Enhancers	NHDF-Ad	bronchial
28	chr9:108207400-108208000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:108207400-108208000	Enhancers	Adipose Nuclei	Adipose
30	chr9:108207400-108208000	Enhancers	Duodenum Mucosa	Duodenum
31	chr9:108207400-108208000	Enhancers	Left Ventricle	heart
32	chr9:108207400-108208200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:108207400-108208200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:108207400-108208200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr9:108207400-108208400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr9:108207400-108208400	Enhancers	Brain Cingulate Gyrus	brain
37	chr9:108207400-108208400	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr9:108207400-108208400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:108207400-108208400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr9:108207400-108208400	Flanking Active TSS	HepG2	liver
41	chr9:108207400-108208600	Enhancers	Brain Hippocampus Middle	brain
42	chr9:108207400-108208800	Enhancers	Fetal Muscle Trunk	muscle
43	chr9:108207600-108208000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr9:108207600-108208000	Enhancers	Osteobl	bone
45	chr9:108207600-108208200	Enhancers	Stomach Smooth Muscle	stomach
46	chr9:108207600-108208400	Enhancers	Brain Anterior Caudate	brain
47	chr9:108207800-108208000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:108207800-108208000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:108207800-108208000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr9:108207800-108208000	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links