Variant report

Variant	rs13244715
Chromosome Location	chr7:108000837-108000838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107998008..108001072-chr7:108096682..108098603,3	MCF-7	breast:
2	chr7:107999436..108001521-chr7:108002531..108004980,2	K562	blood:
3	chr7:107998919..108001119-chr9:140083490..140085157,2	MCF-7	breast:
4	chr7:107999225..108000845-chr7:108077774..108079837,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016149	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12531089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12539530	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12539964	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs13230316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13242951	0.82[MEX][hapmap]
rs16872495	0.82[MEX][hapmap]
rs17155518	0.82[MEX][hapmap]
rs1990712	0.83[EUR][1000 genomes]
rs2080489	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2216259	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs2284285	0.81[JPT][hapmap]
rs2284286	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300027	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395961	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs2395962	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs34294071	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34427132	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35669142	0.89[EUR][1000 genomes]
rs36063908	0.88[EUR][1000 genomes]
rs56102707	0.86[EUR][1000 genomes]
rs6948554	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6957056	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6975557	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription 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
rs13244715	LRRN3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107988000-108001000	Weak transcription	HSMMtube	muscle
2	chr7:107992600-108007400	Weak transcription	HUVEC	blood vessel
3	chr7:107998800-108003800	Weak transcription	Pancreas	Pancrea
4	chr7:107999200-108008800	Weak transcription	Brain Anterior Caudate	brain
5	chr7:107999200-108011200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:107999400-108003600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:107999400-108003800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:107999600-108003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:107999600-108009000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:108000000-108008400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:108000000-108008400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:108000200-108001000	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:108000200-108001200	Weak transcription	Fetal Intestine Small	intestine
14	chr7:108000400-108001200	Enhancers	Adipose Nuclei	Adipose
15	chr7:108000600-108002600	Weak transcription	A549	lung
16	chr7:108000800-108002800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links