Variant report

Variant	rs1449305
Chromosome Location	chr3:100713127-100713128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10936459	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936460	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap]
rs13062274	0.87[ASN][1000 genomes]
rs13066740	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13072542	0.87[ASN][1000 genomes]
rs13075849	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079773	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13080505	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082728	0.87[ASN][1000 genomes]
rs13090397	0.87[ASN][1000 genomes]
rs13091963	0.98[ASN][1000 genomes]
rs1349198	0.83[CHB][hapmap]
rs1449300	0.87[ASN][1000 genomes]
rs1449302	0.87[ASN][1000 genomes]
rs1449306	0.84[CHB][hapmap];0.83[YRI][hapmap]
rs1449308	0.85[CHB][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap]
rs1449309	1.00[YRI][hapmap]
rs1449315	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449320	0.87[ASN][1000 genomes]
rs16843113	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843148	0.87[ASN][1000 genomes]
rs16843163	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254374	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2595914	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2595917	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2713757	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2713768	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713769	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713771	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2713773	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2713774	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2713775	0.99[ASN][1000 genomes]
rs2713776	0.99[ASN][1000 genomes]
rs28365990	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873448	0.87[ASN][1000 genomes]
rs34350012	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34587221	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34670326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748077	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35064087	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35290466	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273569	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928060	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap]
rs4928104	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56847573	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58004340	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs749869	0.91[YRI][hapmap]
rs7631509	0.87[ASN][1000 genomes]
rs9849371	1.00[YRI][hapmap]
rs9853097	0.84[CHB][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1449305	C3orf26	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100712600-100713200	Enhancers	NHDF-Ad	bronchial
2	chr3:100712600-100713400	Enhancers	Duodenum Smooth Muscle	Duodenum
3	chr3:100712600-100713800	Enhancers	Colon Smooth Muscle	Colon
4	chr3:100712600-100714200	Enhancers	Fetal Stomach	stomach
5	chr3:100712800-100713200	Enhancers	Fetal Intestine Large	intestine
6	chr3:100712800-100713200	Enhancers	Fetal Lung	lung
7	chr3:100712800-100714000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:100713000-100713200	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr3:100713000-100713400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:100713000-100713800	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:100713000-100714000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:100713000-100714200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:100713000-100714600	Enhancers	Rectal Smooth Muscle	rectum

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