Variant report

Variant	rs4742950
Chromosome Location	chr9:108283839-108283840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:36275899..36279251-chr9:108280657..108284109,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266264	Chromatin interaction
ENSG00000174373	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1018847	0.97[AMR][1000 genomes];0.96[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12115847	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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]
rs17308339	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]
rs17309137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17309319	0.87[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];0.91[EUR][1000 genomes]
rs2068267	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2771037	0.86[AMR][1000 genomes];0.90[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];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2812299	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812300	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812301	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812302	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2812304	0.86[AMR][1000 genomes];0.90[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];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2812311	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812312	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34787999	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41277785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742649	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742651	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742653	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742654	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs4742946	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4742949	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742952	0.90[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];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[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	0.90[CEU][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes]
rs57432946	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57597571	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59474306	0.86[EUR][1000 genomes]
rs60126815	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62575093	0.86[AMR][1000 genomes];0.87[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];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575102	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575104	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575105	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575106	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575112	0.84[EUR][1000 genomes]
rs62575114	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62575144	0.90[EUR][1000 genomes]
rs62575145	0.91[EUR][1000 genomes]
rs7024265	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7035783	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7037972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7851777	0.95[CEU][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs7872377	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs885954	0.86[YRI][hapmap]
rs9408799	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9409062	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][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	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	nsv982334	chr9:108282762-108289464	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4742950	FSD1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 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	chr9:108269800-108286200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:108272800-108304600	Weak transcription	NHEK	skin
8	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
9	chr9:108276200-108309200	Weak transcription	Lung	lung
10	chr9:108278000-108292800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:108278200-108284000	Weak transcription	Adipose Nuclei	Adipose
12	chr9:108278800-108286600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:108278800-108296600	Weak transcription	A549	lung
14	chr9:108278800-108297000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:108278800-108305800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:108279000-108284600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:108279000-108290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:108279000-108293200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr9:108279000-108296000	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:108279000-108311400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:108279000-108317600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:108279200-108297400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:108279200-108313000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:108279400-108296800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:108279600-108294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:108279600-108296800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:108280200-108285400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:108280200-108289600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:108280200-108289800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:108280200-108297200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:108282400-108284800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:108282400-108288400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:108282400-108289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:108282400-108290400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:108282400-108292200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:108282400-108293200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:108282400-108294200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:108282400-108294800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr9:108282400-108294800	Weak transcription	NH-A	brain
40	chr9:108282400-108296400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:108282400-108296800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:108282400-108296800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:108282400-108297600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:108282400-108299600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:108282400-108300000	Weak transcription	HSMMtube	muscle
46	chr9:108282400-108302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:108282400-108302800	Weak transcription	HSMM	muscle
48	chr9:108282400-108312400	Weak transcription	HepG2	liver
49	chr9:108282400-108319800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:108282400-108319800	Weak transcription	Left Ventricle	heart

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