Variant report

Variant	rs1995152
Chromosome Location	chr1:222769593-222769594
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222768595..222770537-chr1:222773766..222776283,2	K562	blood:
2	chr1:222769042..222774678-chr1:222788731..222793044,4	MCF-7	breast:
3	chr1:222767496..222770287-chr1:222772054..222773560,2	K562	blood:
4	chr1:222768033..222769631-chr1:222786582..222789265,2	K562	blood:
5	chr1:222767462..222770029-chr1:222816956..222818586,2	K562	blood:
6	chr1:222769036..222771053-chr1:222772761..222776622,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11485178	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11485180	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11487813	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1319392	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1603742	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17163214	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1909192	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133185	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173401	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378583	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936031	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936034	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936035	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936037	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936048	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002151	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3008641	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008644	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400619	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1995152	GPATCH2	cis	cerebellum	SCAN
rs1995152	LOC400804	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222764000-222773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:222764200-222769800	Weak transcription	Fetal Heart	heart
3	chr1:222769200-222773600	Enhancers	Stomach Mucosa	stomach

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