Variant report

Variant	rs13205022
Chromosome Location	chr6:56740418-56740419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1044670	1.00[ASW][hapmap]
rs13190784	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs13191084	0.89[EUR][1000 genomes]
rs13195825	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13198484	0.86[AFR][1000 genomes]
rs13198597	0.80[CEU][hapmap]
rs13199024	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13199233	0.88[EUR][1000 genomes]
rs13200166	1.00[MEX][hapmap]
rs13203600	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13207768	1.00[ASW][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs13209099	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13214032	0.93[AFR][1000 genomes]
rs13215865	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13215883	0.80[CEU][hapmap]
rs13216793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13218913	1.00[MEX][hapmap]
rs13220510	0.93[AFR][1000 genomes]
rs1460561	0.93[AFR][1000 genomes]
rs1599280	1.00[ASW][hapmap]
rs16888171	0.89[MEX][hapmap]
rs16888186	0.86[CEU][hapmap]
rs16888189	0.86[CEU][hapmap]
rs16888192	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs17684784	0.89[MEX][hapmap]
rs17684802	1.00[MEX][hapmap]
rs17684878	0.89[MEX][hapmap];0.84[TSI][hapmap]
rs17685045	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17685143	0.93[AFR][1000 genomes]
rs17685277	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[AFR][1000 genomes]
rs17685338	0.93[AFR][1000 genomes]
rs17685380	0.93[AFR][1000 genomes]
rs17751682	0.89[MEX][hapmap]
rs17751695	0.89[MEX][hapmap]
rs17752106	0.81[CEU][hapmap]
rs1870638	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1903330	1.00[LWK][hapmap];0.93[AFR][1000 genomes]
rs1903332	0.80[CEU][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs28360537	0.93[AFR][1000 genomes]
rs28360538	0.93[AFR][1000 genomes]
rs34009699	0.93[AFR][1000 genomes]
rs34027274	0.93[AFR][1000 genomes]
rs34232358	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34399458	0.93[AFR][1000 genomes]
rs34616943	0.93[AFR][1000 genomes]
rs34714091	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34733863	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs36112505	0.93[AFR][1000 genomes]
rs3957366	1.00[ASW][hapmap]
rs4074101	0.89[MEX][hapmap]
rs4299824	1.00[MEX][hapmap]
rs4415160	1.00[MEX][hapmap]
rs4443500	0.89[EUR][1000 genomes]
rs60563401	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67063738	0.86[EUR][1000 genomes]
rs6905658	0.99[EUR][1000 genomes]
rs6911654	0.88[EUR][1000 genomes]
rs6918949	0.89[MEX][hapmap];0.84[TSI][hapmap]
rs6925518	0.99[EUR][1000 genomes]
rs6926742	0.98[EUR][1000 genomes]
rs71550519	0.93[AFR][1000 genomes]
rs71564864	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71564866	0.93[AFR][1000 genomes]
rs71564868	0.81[AFR][1000 genomes]
rs720884	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[AFR][1000 genomes]
rs73457800	0.83[EUR][1000 genomes]
rs7744240	0.93[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs7744799	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7758867	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs7760385	0.93[AFR][1000 genomes]
rs7761501	1.00[MEX][hapmap];0.84[TSI][hapmap]
rs7761729	0.89[MEX][hapmap];0.84[TSI][hapmap]
rs9464401	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv965728	chr6:56733888-56740633	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv508408	chr6:56735681-56773285	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13205022	RAB23	cis	multi-tissue	Pritchard
rs13205022	BMP5	cis	cerebellum	SCAN
rs13205022	DST	cis	cerebellum	SCAN
rs13205022	BEND6	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56734200-56755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:56734600-56750200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:56734600-56755400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:56734800-56740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:56734800-56740600	Weak transcription	NHLF	lung
6	chr6:56734800-56754200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:56734800-56754400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:56735200-56740600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:56735600-56740800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:56736400-56755800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:56738200-56743000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:56740400-56740600	Enhancers	HepG2	liver
13	chr6:56740400-56740800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr6:56740400-56741400	Enhancers	Fetal Intestine Large	intestine
15	chr6:56740400-56741600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr6:56740400-56741600	Flanking Active TSS	A549	lung
17	chr6:56740400-56742000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:56740400-56742000	Genic enhancers	NHDF-Ad	bronchial

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