Variant report

Variant	rs9630290
Chromosome Location	chr12:106332850-106332851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106331505..106334070-chr12:106336834..106339548,2	MCF-7	breast:
2	chr12:106332698..106335575-chr12:106336586..106338838,3	K562	blood:
3	chr12:106322923..106333063-chr12:106528610..106534226,20	MCF-7	breast:
4	chr12:106316278..106317895-chr12:106330750..106333564,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074590	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11112808	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112810	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112812	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112815	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11608722	0.95[ASN][1000 genomes]
rs11837217	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11837987	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12297788	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12425164	0.99[ASN][1000 genomes]
rs12426802	0.95[ASN][1000 genomes]
rs12582103	0.99[ASN][1000 genomes]
rs12810562	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814823	0.95[ASN][1000 genomes]
rs12815201	0.95[ASN][1000 genomes]
rs12816747	0.95[ASN][1000 genomes]
rs12818417	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12833614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1344566	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1344567	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345543	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1421454	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1421456	0.81[AMR][1000 genomes]
rs1421457	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1421458	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1421459	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1895105	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1895106	0.95[ASN][1000 genomes]
rs2032772	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080755	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539238	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539239	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539240	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539241	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539242	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7304960	0.85[AFR][1000 genomes]
rs7312545	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953002	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953243	0.99[ASN][1000 genomes]
rs7955474	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958273	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960459	0.95[ASN][1000 genomes]
rs7961513	0.95[ASN][1000 genomes]
rs7965501	0.99[ASN][1000 genomes]
rs7969437	0.99[ASN][1000 genomes]
rs7971140	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7971261	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7973513	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9630290	C12orf45	cis	parietal	SCAN
rs9630290	CCDC53	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106325400-106336600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:106325600-106335200	Enhancers	HMEC	breast
3	chr12:106327200-106335000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:106328200-106339200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:106328600-106335000	Enhancers	NHEK	skin
6	chr12:106330600-106334000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:106331000-106337200	Weak transcription	HSMM	muscle
8	chr12:106331000-106337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:106331800-106334800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:106332000-106333000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr12:106332000-106333200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:106332200-106337200	Weak transcription	HSMMtube	muscle
13	chr12:106332400-106334000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:106332600-106333000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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