Variant report

Variant	rs4236542
Chromosome Location	chr7:98836916-98836917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10261416	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10274646	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10953286	0.82[MEX][hapmap]
rs11769698	0.92[CEU][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12705056	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4236541	0.97[ASN][1000 genomes]
rs4623337	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624956	0.98[ASN][1000 genomes]
rs4729523	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs6966842	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6969297	0.95[ASN][1000 genomes]
rs6969440	0.95[ASN][1000 genomes]
rs7792178	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7797978	0.95[ASN][1000 genomes]
rs9769317	0.80[AMR][1000 genomes];0.93[EUR][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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4236542	CPSF4	cis	parietal	SCAN
rs4236542	GATS	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98823800-98849600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:98827400-98842000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:98836400-98837000	Active TSS	Gastric	stomach

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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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