Variant report

Variant	rs275999
Chromosome Location	chr12:59848903-59848904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10506395	0.84[CEU][hapmap]
rs10732745	0.94[CEU][hapmap]
rs10735880	0.84[CEU][hapmap]
rs10747850	0.84[CEU][hapmap]
rs10747851	0.84[CEU][hapmap]
rs10747852	0.84[CEU][hapmap]
rs10877315	0.84[CEU][hapmap]
rs276036	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs276038	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs276039	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs276048	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs276069	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276073	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371333	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs373397	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs420644	0.89[CEU][hapmap];0.89[CHD][hapmap]
rs440179	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs444903	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933300	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581257	0.84[CEU][hapmap]
rs6581260	0.84[CEU][hapmap]
rs6581261	0.84[CEU][hapmap]
rs7133515	0.84[CEU][hapmap]
rs7133612	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv735	chr12:59799232-59882716	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv826392	chr12:59805637-59895803	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv899129	chr12:59820966-59941423	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs275999	DTX3	cis	cerebellum	SCAN
rs275999	NXPH4	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59846800-59853400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:59847600-59853000	Weak transcription	HSMM	muscle
3	chr12:59847800-59853000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:59847800-59853200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:59847800-59853200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:59848200-59852800	Weak transcription	NHDF-Ad	bronchial

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