Variant report

Variant	rs1945829
Chromosome Location	chr11:83835601-83835602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10501554	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10501556	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs10898221	0.82[CEU][hapmap]
rs11233903	0.81[GIH][hapmap]
rs11233909	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11233910	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11233914	0.82[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11233916	0.82[CEU][hapmap];0.95[EUR][1000 genomes]
rs11233921	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11233925	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11233926	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11233928	0.89[EUR][1000 genomes]
rs11233929	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11233934	0.82[EUR][1000 genomes]
rs11233938	0.89[EUR][1000 genomes]
rs11233966	0.82[CEU][hapmap]
rs12360734	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs12365077	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17563401	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs17563429	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs57803795	0.85[AFR][1000 genomes]
rs58773272	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59144272	0.97[EUR][1000 genomes]
rs60034832	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60761480	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7106126	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7125922	0.90[EUR][1000 genomes]
rs73515766	0.90[EUR][1000 genomes]
rs73515768	0.90[EUR][1000 genomes]
rs7927940	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs7946613	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039924	chr11:83662904-83993497	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv541102	chr11:83662904-83993497	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv898029	chr11:83717887-83939591	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv2751034	chr11:83801970-83840272	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv1051279	chr11:83818647-83872815	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv555609	chr11:83822181-83842498	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
7	esv2760422	chr11:83828680-83845579	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
8	nsv430414	chr11:83830452-83840252	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
9	nsv516717	chr11:83831259-83842498	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
10	nsv972931	chr11:83831335-83836670	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
11	nsv555610	chr11:83831922-83842498	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1945829	MMP20	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83831200-83839600	Weak transcription	Brain Anterior Caudate	brain
2	chr11:83834400-83835800	Enhancers	Brain Cingulate Gyrus	brain
3	chr11:83834600-83839600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:83834800-83838400	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:83835200-83838600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:83835400-83842000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:83835600-83836600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links