Variant report

Variant	rs960501
Chromosome Location	chr1:57539130-57539131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57531940..57535705-chr1:57536134..57539998,5	K562	blood:
2	chr1:57537146..57539862-chr1:57547524..57549494,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11206965	0.98[ASN][1000 genomes]
rs11206967	0.88[ASN][1000 genomes]
rs11206968	0.83[ASN][1000 genomes]
rs11206969	0.88[ASN][1000 genomes]
rs11206970	0.88[ASN][1000 genomes]
rs11206971	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11206973	0.82[JPT][hapmap]
rs12025887	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12026247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12028404	0.87[ASN][1000 genomes]
rs12038933	0.97[ASN][1000 genomes]
rs12043593	0.87[ASN][1000 genomes]
rs12043848	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12131230	0.99[ASN][1000 genomes]
rs12140416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12565535	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3729546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3738555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3738556	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3754260	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs3754261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3754262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3768176	0.82[JPT][hapmap]
rs3768183	0.88[ASN][1000 genomes]
rs3768184	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs3768185	0.88[ASN][1000 genomes]
rs3768187	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3768188	0.87[ASN][1000 genomes]
rs3768189	0.87[ASN][1000 genomes]
rs3768190	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768192	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3768194	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3820576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3820577	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs514550	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6660463	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs960501	MYSM1	cis	parietal	SCAN
rs960501	DAB1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57530800-57548000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:57534000-57551000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:57534000-57552600	Weak transcription	Fetal Intestine Large	intestine
4	chr1:57537800-57539200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr1:57538000-57539400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:57538600-57550400	Weak transcription	Fetal Brain Male	brain
7	chr1:57539000-57543400	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links