Variant report

Variant	rs2812312
Chromosome Location	chr9:108251400-108251401
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

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

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

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2812312	FSD1L	Cis_1M	lymphoblastoid	RTeQTL
rs2812312	FKTN	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
5	chr9:108221000-108266000	Weak transcription	NHEK	skin
6	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
7	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:108222200-108277000	Weak transcription	Ovary	ovary
9	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
10	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
11	chr9:108223200-108252600	Weak transcription	K562	blood
12	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:108227400-108271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:108228000-108258800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr9:108228400-108252400	Weak transcription	Fetal Intestine Large	intestine
17	chr9:108228400-108257600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:108231400-108257000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:108231800-108254400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:108232000-108252200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:108232600-108268800	Weak transcription	Fetal Brain Female	brain
23	chr9:108233000-108255000	Weak transcription	Dnd41	blood
24	chr9:108233400-108253000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:108233400-108253000	Weak transcription	Hela-S3	cervix
26	chr9:108233600-108269200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:108233600-108272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:108233600-108272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:108233600-108277000	Weak transcription	Adipose Nuclei	Adipose
30	chr9:108236400-108259000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:108237800-108259200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:108239000-108253800	Weak transcription	NHDF-Ad	bronchial
33	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
34	chr9:108243400-108252400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr9:108245200-108251600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:108246400-108261200	Weak transcription	GM12878-XiMat	blood
37	chr9:108247800-108253200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:108247800-108271600	Weak transcription	NH-A	brain
39	chr9:108248000-108251600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:108248000-108260000	Weak transcription	HepG2	liver
41	chr9:108248000-108276000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:108249400-108251600	Strong transcription	HMEC	breast
43	chr9:108249800-108251400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:108249800-108251400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:108250200-108251800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:108250600-108251600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:108250600-108257000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:108250600-108257000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr9:108250600-108263200	Weak transcription	A549	lung
50	chr9:108250600-108268800	Weak transcription	HSMM	muscle

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