Variant report

Variant	rs989531
Chromosome Location	chr2:173933618-173933619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173909580..173911400-chr2:173932850..173935097,2	MCF-7	breast:
2	chr2:173931458..173934623-chr2:173936258..173938174,3	MCF-7	breast:
3	chr2:173930762..173936707-chr2:173937073..173941101,12	MCF-7	breast:
4	chr2:173913477..173915718-chr2:173932935..173935387,2	MCF-7	breast:
5	chr2:173895508..173897322-chr2:173932980..173934730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10180382	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930577	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs11681384	0.96[ASN][1000 genomes]
rs11692252	0.92[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545516	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17760899	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2034647	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2044515	0.86[ASN][1000 genomes]
rs2358084	0.94[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754745	0.82[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs3754748	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769207	0.86[ASN][1000 genomes]
rs6718374	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733082	0.83[ASN][1000 genomes]
rs6735275	0.82[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs6746656	0.82[CHB][hapmap]
rs6758859	0.82[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs6759787	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs7558132	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558553	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7573673	0.82[CEU][hapmap]
rs7608532	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9636294	0.91[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs989532	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs990416	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs990417	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs989531	METTL8	cis	parietal	SCAN
rs989531	SCRN3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173920600-173937200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links