Variant report

Variant	rs59485221
Chromosome Location	chr9:16503212-16503213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12003902	1.00[EUR][1000 genomes]
rs12345489	1.00[EUR][1000 genomes]
rs56679915	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56873701	1.00[EUR][1000 genomes]
rs57014573	1.00[EUR][1000 genomes]
rs7025065	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7025366	1.00[EUR][1000 genomes]
rs7025647	1.00[EUR][1000 genomes]
rs7031782	0.90[EUR][1000 genomes]
rs7035471	1.00[EUR][1000 genomes]
rs7042044	1.00[EUR][1000 genomes]
rs73417433	1.00[EUR][1000 genomes]
rs73645989	1.00[EUR][1000 genomes]
rs73645993	0.83[EUR][1000 genomes]
rs7854653	0.81[EUR][1000 genomes]
rs7858780	0.81[EUR][1000 genomes]
rs7858802	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv892646	chr9:16476144-16514375	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS	lncRNA	n/a	inside rSNPs	diseases
6	nsv892647	chr9:16476144-16521534	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv466265	chr9:16484731-16516941	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
8	nsv613670	chr9:16484731-16516941	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59485221	SF1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16471000-16504600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16483200-16513600	Weak transcription	Psoas Muscle	Psoas
3	chr9:16485000-16504800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:16485400-16505000	Weak transcription	HSMMtube	muscle
5	chr9:16485800-16505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:16488200-16504600	Weak transcription	Fetal Stomach	stomach
7	chr9:16488200-16505200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:16488800-16505000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:16489000-16504800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:16494000-16505000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:16494600-16504600	Weak transcription	Fetal Lung	lung
12	chr9:16495200-16509800	Weak transcription	Aorta	Aorta
13	chr9:16497200-16504800	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:16500000-16505000	Enhancers	Osteobl	bone
15	chr9:16500000-16506400	Enhancers	HUVEC	blood vessel
16	chr9:16500200-16506600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:16500400-16514000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:16501600-16504400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:16501600-16504800	Weak transcription	A549	lung
20	chr9:16501800-16504600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:16502000-16504600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:16502000-16505400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:16502200-16503600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr9:16502200-16504000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:16502200-16504000	Weak transcription	Hela-S3	cervix
26	chr9:16502200-16504000	Weak transcription	NHLF	lung
27	chr9:16502200-16505000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:16502200-16505000	Weak transcription	NHEK	skin
29	chr9:16502200-16510000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:16502200-16510000	Weak transcription	HMEC	breast
31	chr9:16502400-16504000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:16502400-16504600	Weak transcription	Ovary	ovary
33	chr9:16502400-16504600	Weak transcription	NH-A	brain
34	chr9:16502400-16504800	Weak transcription	HSMM	muscle
35	chr9:16502400-16505000	Weak transcription	NHDF-Ad	bronchial
36	chr9:16502400-16505200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:16502400-16505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:16502400-16505200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:16502400-16509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:16502800-16503800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:16503000-16503600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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