Variant report

Variant	rs2146117
Chromosome Location	chr1:152416909-152416910
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152371233..152372113-chr1:152416581..152417372,2	MCF-7	breast:
2	chr1:152416762..152419468-chr1:152419626..152422277,3	MCF-7	breast:
3	chr1:152414849..152417145-chr1:152419655..152422023,2	K562	blood:
4	chr1:152412473..152414075-chr1:152416605..152419173,2	K562	blood:

Variant related genes	Relation type
ENSG00000183586	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10888486	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs11577946	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11579266	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12029431	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs12049036	0.83[CEU][hapmap]
rs12067942	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16834090	0.80[GIH][hapmap]
rs1923493	0.83[CEU][hapmap]
rs1923501	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36061814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753443	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs3753444	0.83[CEU][hapmap]
rs3829868	0.83[CEU][hapmap]
rs4285700	0.83[CEU][hapmap]
rs4845771	0.86[CHD][hapmap];0.80[GIH][hapmap]
rs56325026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72698953	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72698960	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72698963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72698964	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72698999	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7521839	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv824664	chr1:152409024-152434443	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv463850	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv547858	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872445	chr1:152411813-152440753	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2146117	GABPB2	cis	cerebellum	SCAN
rs2146117	CRNN	cis	Esophagus Mucosa	GTEx
rs2146117	AQP10	cis	parietal	SCAN
rs2146117	IVL	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152413800-152417000	Enhancers	Esophagus	oesophagus
2	chr1:152413800-152417000	Enhancers	Stomach Mucosa	stomach
3	chr1:152415600-152420000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:152415800-152417000	Enhancers	Brain Hippocampus Middle	brain
5	chr1:152415800-152417000	Enhancers	Brain Substantia Nigra	brain
6	chr1:152416000-152417600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:152416400-152417000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:152416400-152420000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:152416400-152423800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:152416600-152417000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:152416800-152419800	Weak transcription	Rectal Smooth Muscle	rectum

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