Variant report

Variant	rs9395943
Chromosome Location	chr6:54228152-54228153
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54221394..54223737-chr6:54226905..54229813,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10456174	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10456681	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10456682	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10484642	1.00[CEU][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10498797	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10948812	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
rs12189890	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12193891	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12195997	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12204930	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12205456	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12209457	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12209701	1.00[CEU][hapmap]
rs12210322	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12215711	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12661397	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12663327	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12664425	0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16885285	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2063238	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3195579	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3736350	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs45545344	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59459598	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59508393	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62412590	0.82[EUR][1000 genomes]
rs62412614	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62412618	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73446621	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7750024	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7750323	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9283920	0.94[CEU][hapmap]
rs9367566	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9382326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9395949	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9474819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474825	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9395943	GCLC	cis	parietal	SCAN
rs9395943	PAQR8	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54211800-54256200	Weak transcription	Fetal Intestine Large	intestine
2	chr6:54212000-54257400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:54226600-54231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:54226800-54231400	Weak transcription	HMEC	breast
5	chr6:54227200-54231400	Weak transcription	NHEK	skin
6	chr6:54227200-54231600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54227200-54231800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:54228000-54231400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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