Variant report

Variant	rs9660532
Chromosome Location	chr1:227515679-227515680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227514733..227517103-chr1:227519099..227520734,2	K562	blood:
2	chr1:227506088..227508299-chr1:227513676..227515983,2	MCF-7	breast:
3	chr1:227511186..227513689-chr1:227514220..227516640,3	K562	blood:
4	chr1:227504415..227507165-chr1:227514081..227517438,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11800169	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11800364	1.00[ASN][1000 genomes]
rs11800959	1.00[ASN][1000 genomes]
rs11801012	1.00[ASN][1000 genomes]
rs11801282	1.00[ASN][1000 genomes]
rs11801835	0.82[EUR][1000 genomes]
rs11802399	1.00[ASN][1000 genomes]
rs11803651	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11804181	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11804271	0.91[AMR][1000 genomes]
rs11804807	1.00[ASN][1000 genomes]
rs11806721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807068	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807375	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807425	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807957	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808210	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808674	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808696	0.91[AMR][1000 genomes]
rs11809113	1.00[ASN][1000 genomes]
rs11809905	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811210	1.00[ASN][1000 genomes]
rs11811620	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811982	1.00[ASN][1000 genomes]
rs11812048	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34125608	1.00[ASN][1000 genomes]
rs35601687	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36055753	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41270147	1.00[ASN][1000 genomes]
rs6671926	1.00[ASN][1000 genomes]
rs73096355	1.00[ASN][1000 genomes]
rs73096357	1.00[ASN][1000 genomes]
rs7524967	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7530155	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547092	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9660532	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227507000-227515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:227509400-227516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:227510400-227516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:227511600-227518000	Weak transcription	K562	blood
6	chr1:227512000-227516400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:227512000-227523200	Weak transcription	Stomach Mucosa	stomach
8	chr1:227513200-227516200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:227515600-227516000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:227515600-227516800	Enhancers	HepG2	liver
11	chr1:227515600-227517000	Enhancers	Liver	Liver

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