Variant report

Variant	rs1971381
Chromosome Location	chr3:99450469-99450470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10935921	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107242	0.93[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485299	0.88[JPT][hapmap]
rs12486703	0.84[ASN][1000 genomes]
rs12486901	0.88[JPT][hapmap]
rs12494720	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080329	0.95[CHD][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs13088056	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13088851	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13099452	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1492343	0.88[JPT][hapmap]
rs1871847	0.88[JPT][hapmap]
rs28820982	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34218799	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34303842	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906671	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35495890	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35577846	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	0.88[JPT][hapmap]
rs4408901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928143	0.86[JPT][hapmap]
rs4928144	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928219	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928220	0.88[JPT][hapmap]
rs4928222	0.88[JPT][hapmap]
rs55648906	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6800456	0.88[JPT][hapmap]
rs73152013	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613580	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7614366	0.85[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs7632327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1971381	C3orf26	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99440200-99458000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:99440400-99458000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:99440400-99458200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:99440400-99471000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:99441200-99458000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:99441400-99466800	Weak transcription	NH-A	brain
7	chr3:99443400-99471400	Weak transcription	Aorta	Aorta
8	chr3:99448000-99451000	Strong transcription	Osteobl	bone
9	chr3:99448600-99450600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:99449400-99458000	Weak transcription	HSMM	muscle
11	chr3:99449600-99463400	Weak transcription	HUVEC	blood vessel
12	chr3:99449800-99450600	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr3:99450200-99450600	Enhancers	Adipose Nuclei	Adipose
14	chr3:99450400-99450600	Enhancers	HSMMtube	muscle
15	chr3:99450400-99458000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:99450400-99463600	Weak transcription	NHDF-Ad	bronchial
17	chr3:99450400-99463800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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