Variant report

Variant	rs4742953
Chromosome Location	chr9:108335958-108335959
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108330989..108333120-chr9:108334347..108336541,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FSD1L-2	chr9:108335936-108336027	NONHSAT133821

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1018847	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115847	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17250623	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17251166	0.91[CEU][hapmap];0.90[YRI][hapmap];0.93[EUR][1000 genomes]
rs17308339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17309137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17309319	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17309806	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2068267	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2771028	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2771037	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2771039	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2771044	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2771045	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2812298	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812299	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812300	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812301	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812302	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812304	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812306	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2812311	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2812312	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34787999	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41277785	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742649	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742651	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742653	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742654	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs4742946	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742949	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742952	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742954	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4742955	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs4742956	0.91[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57432946	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57597571	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59474306	0.94[EUR][1000 genomes]
rs60126815	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62575093	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62575095	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62575101	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62575102	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62575104	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575105	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575106	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575112	0.88[EUR][1000 genomes]
rs62575114	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575144	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62575145	0.99[EUR][1000 genomes]
rs7024265	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035783	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7037972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851777	0.96[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7872377	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs885954	0.90[YRI][hapmap]
rs9408799	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9409062	0.98[AMR][1000 genomes];0.91[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
rs4742953	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321600-108336000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:108321600-108336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:108321600-108336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:108321600-108338000	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:108321600-108353600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:108321600-108354000	Weak transcription	Right Ventricle	heart
7	chr9:108321600-108360200	Weak transcription	HSMM	muscle
8	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:108324800-108353800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:108325400-108337800	Weak transcription	Dnd41	blood
11	chr9:108325400-108339200	Weak transcription	Fetal Brain Male	brain
12	chr9:108325400-108357200	Weak transcription	A549	lung
13	chr9:108325600-108336600	Weak transcription	Fetal Lung	lung
14	chr9:108325600-108353200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:108325600-108353200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:108325600-108353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:108325800-108353800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:108326000-108338200	Weak transcription	Ovary	ovary
19	chr9:108328000-108372800	Weak transcription	NHEK	skin
20	chr9:108330800-108366200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:108331000-108337400	Weak transcription	Adipose Nuclei	Adipose
22	chr9:108331200-108340000	Weak transcription	NH-A	brain
23	chr9:108332800-108337200	Weak transcription	Osteobl	bone
24	chr9:108333200-108337800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:108333200-108338200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:108333200-108400400	Weak transcription	HMEC	breast
27	chr9:108333400-108336800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:108333400-108352600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:108333400-108352600	Weak transcription	Fetal Kidney	kidney
30	chr9:108333600-108337600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:108334000-108337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:108334200-108368200	Weak transcription	Gastric	stomach
33	chr9:108334400-108336800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:108334600-108337800	Weak transcription	Fetal Intestine Large	intestine
35	chr9:108334600-108338400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:108334800-108337400	Weak transcription	Brain Anterior Caudate	brain
37	chr9:108334800-108353000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:108335000-108336000	Weak transcription	Primary T cells from cord blood	blood
39	chr9:108335000-108336000	Weak transcription	Fetal Brain Female	brain
40	chr9:108335000-108336600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:108335000-108336800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:108335000-108336800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:108335000-108337200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:108335000-108337400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr9:108335000-108338400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:108335000-108339800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:108335000-108352200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:108335000-108352600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr9:108335000-108352600	Weak transcription	Brain Hippocampus Middle	brain
50	chr9:108335000-108353000	Weak transcription	Aorta	Aorta

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