Variant report

Variant	rs12539964
Chromosome Location	chr7:108009267-108009268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108006947..108010062-chr7:108010245..108014925,5	MCF-7	breast:
2	chr7:108007896..108010349-chr7:108095671..108097196,3	MCF-7	breast:
3	chr7:107974565..107976099-chr7:108007204..108009580,2	MCF-7	breast:
4	chr7:108008768..108011253-chr7:108015718..108019224,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1016149	0.83[EUR][1000 genomes]
rs12531089	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs12539530	0.90[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12673082	0.81[MEX][hapmap]
rs12673676	0.81[MEX][hapmap]
rs13230316	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs13244715	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1990712	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2080489	0.84[EUR][1000 genomes]
rs2216259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284286	0.87[EUR][1000 genomes]
rs2284287	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs2284288	0.84[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs2300027	0.90[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs2395961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2395962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34427132	0.83[EUR][1000 genomes]
rs35669142	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36063908	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56102707	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6948554	0.83[EUR][1000 genomes]
rs6975557	0.90[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7804045	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs969708	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12539964	LRRN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107999200-108011200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:108004000-108016600	Weak transcription	Pancreas	Pancrea
3	chr7:108004400-108016600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:108007200-108009400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:108007400-108009400	Enhancers	HUVEC	blood vessel
6	chr7:108008000-108009400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr7:108008000-108010600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:108008400-108009400	Enhancers	Brain Angular Gyrus	brain
9	chr7:108008400-108009400	Enhancers	Brain Cingulate Gyrus	brain
10	chr7:108008400-108009400	Enhancers	Fetal Brain Male	brain
11	chr7:108008400-108009400	Enhancers	HSMM	muscle
12	chr7:108008800-108009400	Enhancers	Brain Anterior Caudate	brain
13	chr7:108008800-108009400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr7:108008800-108009400	Flanking Active TSS	A549	lung
15	chr7:108009000-108009400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:108009200-108010000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:108009200-108012600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links