Variant report

Variant	rs57463531
Chromosome Location	chr1:77134786-77134787
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12723060	0.99[ASN][1000 genomes]
rs12724872	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12738872	0.83[ASN][1000 genomes]
rs2349044	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3748712	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv526433	chr1:77030764-77268215	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1001253	chr1:77077660-77234093	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv870909	chr1:77104773-77195164	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57463531	MSH4,RABGGTB	cis	brain	BrainEAC

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77132600-77137200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:77132600-77138800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:77133400-77136200	Enhancers	Fetal Brain Male	brain
4	chr1:77133600-77135200	Enhancers	Fetal Intestine Small	intestine
5	chr1:77134200-77136200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:77134400-77135200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:77134400-77135200	Enhancers	Liver	Liver
8	chr1:77134600-77136200	Enhancers	Brain Germinal Matrix	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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