Variant report

Variant	rs2395962
Chromosome Location	chr7:108023548-108023549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108022146..108024976-chr7:108095353..108098019,2	MCF-7	breast:
2	chr7:108019480..108021624-chr7:108021812..108023878,2	MCF-7	breast:
3	chr7:107997129..107999645-chr7:108022615..108024810,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction
ENSG00000266112	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

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]
rs12539964	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]
rs12673082	0.81[MEX][hapmap]
rs12673676	0.81[MEX][hapmap]
rs13230316	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs13244715	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17155617	0.81[MKK][hapmap]
rs1990712	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2080489	0.84[EUR][1000 genomes]
rs2216259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2284286	0.87[EUR][1000 genomes]
rs2284287	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs2284288	0.85[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];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34427132	0.83[EUR][1000 genomes]
rs35669142	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36063908	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56102707	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs969708	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2395962	OAT	trans	lymphoblastoid	seeQTL
rs2395962	LRRN3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108014800-108043200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:108020000-108034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:108021400-108040800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:108021400-108043000	Weak transcription	HMEC	breast
5	chr7:108021800-108025000	Weak transcription	A549	lung
6	chr7:108021800-108026600	Weak transcription	HUVEC	blood vessel
7	chr7:108022400-108034200	Weak transcription	Pancreas	Pancrea
8	chr7:108023000-108024000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr7:108023200-108024000	Enhancers	Brain Germinal Matrix	brain
10	chr7:108023200-108024400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr7:108023400-108023600	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr7:108023400-108023600	Enhancers	Brain Anterior Caudate	brain
13	chr7:108023400-108023800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:108023400-108023800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:108023400-108023800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:108023400-108023800	Enhancers	Fetal Brain Male	brain
17	chr7:108023400-108024000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:108023400-108024000	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links