Variant report

Variant	rs12081001
Chromosome Location	chr1:76954003-76954004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11162157	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11162159	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11162163	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11162165	0.92[CEU][hapmap]
rs12063002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12065647	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12066794	0.92[CEU][hapmap]
rs12072202	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12075814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12075927	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12077146	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12085320	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12742787	0.91[ASN][1000 genomes]
rs61771553	0.82[ASN][1000 genomes]
rs6665907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691403	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6693031	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7520183	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526216	0.84[ASN][1000 genomes]
rs7526478	0.82[ASN][1000 genomes]
rs7531740	0.84[EUR][1000 genomes]
rs7536778	0.92[CEU][hapmap]
rs7539513	0.84[EUR][1000 genomes]
rs7544496	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7547235	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7555277	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv462006	chr1:76826279-77042405	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv546585	chr1:76826279-77042405	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv997827	chr1:76929028-77201457	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv462017	chr1:76940156-76982445	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv546586	chr1:76940156-76982445	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
8	nsv462028	chr1:76948044-76976522	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
9	nsv546587	chr1:76948044-76976522	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv462039	chr1:76948044-77019597	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv470718	chr1:76948044-77019597	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv546588	chr1:76948044-77019597	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv462050	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv462062	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv462073	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv546589	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12081001	MALAT1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76948000-76960400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:76950600-76960600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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