Variant report

Variant	rs10484642
Chromosome Location	chr6:54201114-54201115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54177292..54179184-chr6:54200767..54202415,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10456174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs10456681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs10456682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10498797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10948812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948813	1.00[CEU][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10948814	1.00[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12193891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12195997	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12204930	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12205456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12209457	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12209701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12210322	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12215711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12524739	1.00[JPT][hapmap]
rs12661397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12663327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12664425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16885285	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2063238	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3195579	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736350	0.86[EUR][1000 genomes]
rs3777640	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs45545344	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59459598	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59508393	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62412590	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62412614	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62412618	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458979	1.00[JPT][hapmap]
rs73446621	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7750024	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7750323	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9283920	0.94[CEU][hapmap]
rs9367566	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9382325	1.00[CEU][hapmap]
rs9382326	1.00[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs9395943	1.00[CEU][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9395949	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9474819	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9474825	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10484642	PAQR8	cis	cerebellum	SCAN
rs10484642	GSTA4	cis	cerebellum	SCAN
rs10484642	GCLC	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54198800-54202200	Enhancers	HUVEC	blood vessel
2	chr6:54200000-54201600	Enhancers	A549	lung
3	chr6:54200000-54201600	Enhancers	NH-A	brain
4	chr6:54200200-54201200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:54200200-54201200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:54200200-54201200	Enhancers	Hela-S3	cervix
7	chr6:54200200-54201400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:54200200-54201400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:54200200-54201400	Enhancers	HMEC	breast
10	chr6:54200200-54201400	Enhancers	HSMM	muscle
11	chr6:54200200-54201400	Enhancers	NHEK	skin
12	chr6:54200200-54201600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:54200200-54201600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:54200400-54201200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:54200400-54201200	Enhancers	HSMMtube	muscle
16	chr6:54200400-54201400	Enhancers	NHDF-Ad	bronchial
17	chr6:54200400-54201400	Enhancers	NHLF	lung
18	chr6:54200400-54201400	Enhancers	Osteobl	bone
19	chr6:54200400-54201600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:54200600-54201400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links