Variant report

Variant	rs12115847
Chromosome Location	chr9:108262743-108262744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:108262354-108263646	GM12891	blood:	n/a	n/a
2	SPI1	chr9:108262512-108263018	GM12878	blood:	n/a	n/a
3	BCL11A	chr9:108262390-108263043	GM12878	blood:	n/a	n/a
4	STAT3	chr9:108262227-108263135	GM12878	blood:	n/a	n/a
5	TBP	chr9:108262410-108263410	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:108262489-108263206	GM12878	blood:	n/a	n/a
7	STAT5A	chr9:108262642-108263067	GM12878	blood:	n/a	n/a
8	BHLHE40	chr9:108262406-108263321	GM12878	blood:	n/a	n/a
9	ATF2	chr9:108262532-108263181	GM12878	blood:	n/a	n/a
10	MAZ	chr9:108262373-108263156	GM12878	blood:	n/a	n/a
11	SP1	chr9:108262430-108262780	GM12878	blood:	n/a	n/a
12	BATF	chr9:108262499-108263024	GM12878	blood:	n/a	n/a
13	RELA	chr9:108262520-108263379	GM18951	blood:	n/a	n/a
14	WRNIP1	chr9:108262468-108263096	GM12878	blood:	n/a	n/a
15	MTA3	chr9:108262384-108263193	GM12878	blood:	n/a	n/a
16	EP300	chr9:108262319-108263074	GM12878	blood:	n/a	n/a
17	IKZF1	chr9:108262458-108263272	GM12878	blood:	n/a	n/a
18	FOXM1	chr9:108262309-108263154	GM12878	blood:	n/a	n/a
19	POLR2A	chr9:108262731-108263089	GM12892	blood:	n/a	n/a
20	POLR2A	chr9:108262725-108263074	GM12892	blood:	n/a	n/a
21	SPI1	chr9:108262432-108263027	GM12878	blood:	n/a	n/a
22	SPI1	chr9:108262544-108262975	GM12891	blood:	n/a	n/a
23	RCOR1	chr9:108262108-108263393	GM12878	blood:	n/a	n/a
24	RELA	chr9:108262424-108263379	GM12891	blood:	n/a	n/a
25	EP300	chr9:108262530-108263274	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr9:108262407-108263381	GM12878	blood:	n/a	n/a
27	POLR2A	chr9:108262453-108263174	GM12892	blood:	n/a	n/a
28	MXI1	chr9:108262363-108263054	GM12878	blood:	n/a	n/a
29	NFIC	chr9:108262210-108263304	GM12878	blood:	n/a	n/a
30	RELA	chr9:108262496-108263133	GM10847	blood:	n/a	n/a
31	RELA	chr9:108262539-108263335	GM19099	blood:	n/a	n/a
32	RUNX3	chr9:108262382-108263103	GM12878	blood:	n/a	n/a
33	BCL11A	chr9:108262395-108262838	GM12878	blood:	n/a	n/a
34	PML	chr9:108262714-108263100	GM12878	blood:	n/a	n/a
35	PAX5	chr9:108262449-108262794	GM12878	blood:	n/a	n/a
36	CHD2	chr9:108262441-108263098	GM12878	blood:	n/a	n/a
37	SPI1	chr9:108262727-108262927	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:108262661-108263089	GM12891	blood:	n/a	n/a
39	SPI1	chr9:108262685-108263058	GM12891	blood:	n/a	n/a
40	CUX1	chr9:108262469-108263558	GM12878	blood:	n/a	n/a
41	BCLAF1	chr9:108262421-108263189	GM12878	blood:	n/a	chr9:108263127-108263136
42	MEF2A	chr9:108262374-108263164	GM12878	blood:	n/a	n/a
43	ATF2	chr9:108262465-108263203	GM12878	blood:	n/a	n/a
44	STAT1	chr9:108262639-108263023	GM12878	blood:	n/a	n/a
45	RELA	chr9:108262286-108263484	GM12878	blood:	n/a	n/a
46	NFIC	chr9:108262444-108263211	GM12878	blood:	n/a	n/a
47	POLR2A	chr9:108262583-108263180	GM12878	blood:	n/a	n/a
48	ZNF143	chr9:108262701-108263087	GM12878	blood:	n/a	n/a
49	EBF1	chr9:108262522-108263508	GM12878	blood:	n/a	n/a
50	RUNX3	chr9:108262169-108263131	GM12878	blood:	n/a	n/a

No data

Variant related genes	Relation type
FSD1L	TF binding region

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

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

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

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12115847	FSD1L	Cis_1M	lymphoblastoid	RTeQTL
rs12115847	FKTN	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108221000-108266000	Weak transcription	NHEK	skin
3	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
4	chr9:108222200-108277000	Weak transcription	Ovary	ovary
5	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
6	chr9:108227400-108271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:108232600-108268800	Weak transcription	Fetal Brain Female	brain
10	chr9:108233600-108269200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:108233600-108272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:108233600-108272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:108233600-108277000	Weak transcription	Adipose Nuclei	Adipose
14	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
15	chr9:108247800-108271600	Weak transcription	NH-A	brain
16	chr9:108248000-108276000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:108250600-108263200	Weak transcription	A549	lung
18	chr9:108250600-108268800	Weak transcription	HSMM	muscle
19	chr9:108250800-108268800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:108251200-108268600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:108251600-108266400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:108251600-108272000	Weak transcription	HMEC	breast
23	chr9:108251800-108268800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:108257400-108265400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:108257400-108269000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:108257600-108269000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:108258200-108266000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:108258200-108277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:108258200-108282000	Weak transcription	Psoas Muscle	Psoas
30	chr9:108258400-108276800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:108258400-108276800	Weak transcription	Brain Germinal Matrix	brain
32	chr9:108258800-108268800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:108259000-108277000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:108259600-108272200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:108259600-108282000	Weak transcription	HSMMtube	muscle
36	chr9:108259800-108268800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:108260400-108268400	Weak transcription	HepG2	liver
38	chr9:108261600-108265000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:108261800-108263800	Enhancers	Primary B cells from peripheral blood	blood
40	chr9:108261800-108264200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr9:108262000-108264000	Enhancers	Primary B cells from cord blood	blood
42	chr9:108262000-108268000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:108262200-108262800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:108262400-108262800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr9:108262400-108263400	Flanking Active TSS	GM12878-XiMat	blood
46	chr9:108262400-108263600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr9:108262600-108262800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr9:108262600-108262800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:108262600-108263400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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