Variant report

Variant	rs17308339
Chromosome Location	chr9:108296577-108296578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108295821..108298820-chr9:108299705..108303201,3	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

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

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

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv416298	chr9:108295722-108303569	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17308339	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
3	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
5	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
6	chr9:108272800-108304600	Weak transcription	NHEK	skin
7	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
8	chr9:108276200-108309200	Weak transcription	Lung	lung
9	chr9:108278800-108296600	Weak transcription	A549	lung
10	chr9:108278800-108297000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:108278800-108305800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:108279000-108311400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:108279000-108317600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:108279200-108297400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:108279200-108313000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:108279400-108296800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:108279600-108296800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:108280200-108297200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:108282400-108296800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:108282400-108296800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:108282400-108297600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:108282400-108299600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:108282400-108300000	Weak transcription	HSMMtube	muscle
24	chr9:108282400-108302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:108282400-108302800	Weak transcription	HSMM	muscle
26	chr9:108282400-108312400	Weak transcription	HepG2	liver
27	chr9:108282400-108319800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:108282400-108319800	Weak transcription	Left Ventricle	heart
29	chr9:108282400-108319800	Weak transcription	Psoas Muscle	Psoas
30	chr9:108282600-108319800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:108285200-108296800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:108289200-108306200	Weak transcription	Fetal Brain Male	brain
33	chr9:108289800-108309800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:108290000-108298800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr9:108291400-108297200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:108291800-108310200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:108292600-108296800	Weak transcription	NHLF	lung
38	chr9:108292600-108305600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:108292600-108319800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:108293600-108299800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:108293800-108319800	Weak transcription	Liver	Liver
42	chr9:108294000-108297000	Weak transcription	Adipose Nuclei	Adipose
43	chr9:108294400-108304400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:108294600-108296800	Weak transcription	GM12878-XiMat	blood
45	chr9:108294600-108299600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr9:108294600-108305200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:108294800-108297400	Weak transcription	HMEC	breast
48	chr9:108294800-108312000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:108294800-108319800	Weak transcription	Hela-S3	cervix
50	chr9:108295000-108296600	Weak transcription	Osteobl	bone

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