Variant report

Variant	rs1816854
Chromosome Location	chr12:44205018-44205019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:44199857..44202613-chr12:44203526..44207963,8	K562	blood:
2	chr12:44203878..44205579-chr12:44209943..44211835,2	K562	blood:
3	chr12:44151664..44154111-chr12:44204894..44207350,2	K562	blood:
4	chr12:44203831..44205856-chr12:44214140..44216950,2	MCF-7	breast:
5	chr12:44162830..44166263-chr12:44204627..44207317,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198001	Chromatin interaction
ENSG00000129317	Chromatin interaction
ENSG00000151239	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10506231	0.94[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10880569	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880571	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10880574	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs11182268	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs11182269	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[ASN][1000 genomes]
rs11182270	0.94[ASN][1000 genomes]
rs11182273	0.88[ASW][hapmap];0.94[CEU][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11182275	0.94[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11182279	0.94[ASN][1000 genomes]
rs11182280	0.94[CEU][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11182281	0.95[ASN][1000 genomes]
rs11182282	0.90[ASN][1000 genomes]
rs11182284	0.89[ASN][1000 genomes]
rs11182286	0.81[ASN][1000 genomes]
rs11182287	0.89[ASN][1000 genomes]
rs11182288	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11182289	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11182290	0.83[AFR][1000 genomes]
rs11182291	0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs11556066	0.94[ASN][1000 genomes]
rs11608602	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12226960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12228995	0.86[ASN][1000 genomes]
rs12230695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12231553	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs12829856	0.94[ASN][1000 genomes]
rs28437935	0.85[ASN][1000 genomes]
rs35980560	0.94[ASN][1000 genomes]
rs3764004	0.94[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4251562	0.89[ASN][1000 genomes]
rs61290421	0.81[ASN][1000 genomes]
rs73093785	0.94[ASN][1000 genomes]
rs7966902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1816854	PUS7L	cis	cerebellum	SCAN
rs1816854	PUS7L	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44201000-44205800	Weak transcription	HMEC	breast
2	chr12:44201000-44207400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:44201200-44206200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:44201400-44209400	Weak transcription	Fetal Intestine Small	intestine
5	chr12:44201600-44205200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:44201800-44205400	Weak transcription	NHEK	skin
7	chr12:44202000-44217800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:44202200-44205400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:44204400-44205600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:44204600-44205400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr12:44204600-44206000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:44204800-44205200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr12:44205000-44206200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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