Variant report

Variant	rs9839078
Chromosome Location	chr3:115802317-115802318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11425708	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918080	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695319	0.80[ASN][1000 genomes]
rs13100914	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13315058	0.80[ASN][1000 genomes]
rs13318106	0.88[TSI][hapmap]
rs1344131	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17630430	0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17697994	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920360	0.80[ASN][1000 genomes]
rs1920379	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091669	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222827	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864060	1.00[JPT][hapmap]
rs2864066	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2864067	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28735793	0.83[ASN][1000 genomes]
rs33956431	0.89[ASN][1000 genomes]
rs34523792	0.82[ASN][1000 genomes]
rs34543919	0.80[ASN][1000 genomes]
rs34844901	0.89[ASN][1000 genomes]
rs34930794	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35080450	0.80[ASN][1000 genomes]
rs35242629	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35619123	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35780065	0.89[ASN][1000 genomes]
rs35914238	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4263291	0.98[ASN][1000 genomes]
rs4831121	0.80[ASN][1000 genomes]
rs4831225	0.81[GIH][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4831226	0.80[ASN][1000 genomes]
rs4831227	0.89[ASN][1000 genomes]
rs4831228	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4831229	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4831230	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5004406	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56121547	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62269168	0.98[ASN][1000 genomes]
rs62269170	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62271281	0.80[ASN][1000 genomes]
rs66490447	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765355	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772113	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139202	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632265	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637650	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289042	0.88[ASN][1000 genomes]
rs9809229	0.83[TSI][hapmap]
rs9813038	0.88[ASN][1000 genomes]
rs9816425	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821040	0.81[GIH][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs9821865	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822568	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824605	0.81[GIH][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs9836963	0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9837276	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9851643	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9854345	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9854711	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855097	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857520	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858539	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs9866484	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868706	0.80[ASN][1000 genomes]
rs9873576	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9877662	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878559	0.80[ASN][1000 genomes]
rs9985471	0.86[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][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	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9839078	FSTL1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115780400-115830000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:115780600-115803800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:115799400-115806000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:115800000-115802600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:115801200-115821400	Weak transcription	Fetal Lung	lung
6	chr3:115802000-115804200	Enhancers	NHEK	skin
7	chr3:115802000-115807000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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