Variant report

Variant	rs41277785
Chromosome Location	chr9:108312158-108312159
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108310997..108313277-chr9:108319909..108321430,2	K562	blood:
2	chr9:108312149..108315123-chr9:108317166..108320384,3	K562	blood:
3	chr9:108311203..108313649-chr9:108317166..108319459,2	K562	blood:

Variant related genes	Relation type
ENSG00000106692	Chromatin interaction
ENSG00000228317	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1018847	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10491808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12115847	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17250623	0.88[EUR][1000 genomes]
rs17251166	0.86[EUR][1000 genomes]
rs17308339	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17309137	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17309319	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17309806	0.91[EUR][1000 genomes]
rs2068267	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2771028	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2771037	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2771039	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2771044	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2771045	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2812298	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2812299	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2812300	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2812301	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2812302	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2812304	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2812306	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2812309	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2812311	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2812312	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34787999	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742649	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742651	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742653	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742654	0.85[EUR][1000 genomes]
rs4742946	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4742949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742952	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742953	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742954	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742955	0.89[EUR][1000 genomes]
rs4742956	0.91[EUR][1000 genomes]
rs57432946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57597571	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59474306	0.87[EUR][1000 genomes]
rs60126815	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62575093	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62575095	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575101	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62575102	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62575104	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575106	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575112	0.85[EUR][1000 genomes]
rs62575114	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62575144	0.90[EUR][1000 genomes]
rs62575145	0.91[EUR][1000 genomes]
rs7024265	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035783	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7037972	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7851777	0.88[EUR][1000 genomes]
rs7872377	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9408799	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9409062	0.97[AMR][1000 genomes];0.97[EUR][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	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	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
rs41277785	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108279000-108317600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:108279200-108313000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:108282400-108312400	Weak transcription	HepG2	liver
4	chr9:108282400-108319800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:108282400-108319800	Weak transcription	Left Ventricle	heart
6	chr9:108282400-108319800	Weak transcription	Psoas Muscle	Psoas
7	chr9:108282600-108319800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:108292600-108319800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:108293800-108319800	Weak transcription	Liver	Liver
10	chr9:108294800-108319800	Weak transcription	Hela-S3	cervix
11	chr9:108295600-108319800	Weak transcription	Aorta	Aorta
12	chr9:108296400-108316200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:108297600-108319800	Weak transcription	NHLF	lung
14	chr9:108297800-108319200	Weak transcription	Dnd41	blood
15	chr9:108297800-108319800	Weak transcription	Adipose Nuclei	Adipose
16	chr9:108298000-108319800	Weak transcription	NHDF-Ad	bronchial
17	chr9:108298400-108312200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:108298600-108316000	Weak transcription	Fetal Brain Female	brain
19	chr9:108298800-108314000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:108298800-108314400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:108298800-108319800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:108300200-108316200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:108300400-108313200	Weak transcription	HSMMtube	muscle
24	chr9:108301000-108319800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:108301400-108319800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:108302200-108319800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:108304400-108314200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:108304400-108319800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:108305000-108319800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:108305600-108314200	Weak transcription	Fetal Kidney	kidney
31	chr9:108305800-108319200	Weak transcription	GM12878-XiMat	blood
32	chr9:108305800-108319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:108307200-108312800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:108307200-108319800	Weak transcription	Ovary	ovary
35	chr9:108309000-108319800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:108309200-108319600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:108309200-108319800	Weak transcription	HMEC	breast
38	chr9:108309400-108319800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:108309600-108319800	Weak transcription	A549	lung
40	chr9:108310400-108319400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:108311000-108313400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:108311000-108313800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:108312000-108319800	Weak transcription	HSMM	muscle
44	chr9:108312000-108319800	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links