Variant report

Variant	rs6049798
Chromosome Location	chr20:24572046-24572047
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16986777	0.86[JPT][hapmap]
rs16986779	0.86[JPT][hapmap]
rs4087431	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4815280	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815281	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs4815283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036843	0.96[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6036845	0.80[ASN][1000 genomes]
rs6036846	0.86[JPT][hapmap]
rs6036850	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049796	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6049803	0.82[JPT][hapmap]
rs6049804	0.86[JPT][hapmap]
rs6049811	0.88[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs6114791	0.86[JPT][hapmap]
rs7271447	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs742803	0.86[JPT][hapmap]

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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6049798	CST8	cis	cerebellum	SCAN
rs6049798	PLK1S1	cis	parietal	SCAN
rs6049798	ACSS1	cis	parietal	SCAN
rs6049798	MBIP	trans	cerebellum	SCAN
rs6049798	MFSD5	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24568200-24574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24568200-24577400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:24568800-24573800	Weak transcription	Fetal Heart	heart
4	chr20:24568800-24575800	Weak transcription	Brain Substantia Nigra	brain
5	chr20:24569200-24573800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr20:24571400-24584800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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