Variant report

Variant	rs2971544
Chromosome Location	chr3:118980188-118980189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10934489	0.81[ASN][1000 genomes]
rs11916079	0.83[ASN][1000 genomes]
rs1542233	0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs2594727	0.82[AMR][1000 genomes]
rs2717266	0.89[AMR][1000 genomes]
rs4687993	0.90[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs56269733	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6438517	0.81[ASN][1000 genomes]
rs6775982	0.84[ASN][1000 genomes]
rs6800377	0.83[ASN][1000 genomes]
rs6800491	0.84[ASN][1000 genomes]
rs7620780	0.93[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs7622994	0.93[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs7625392	0.80[MEX][hapmap]
rs9834125	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2971544	CD86	cis	cerebellum	SCAN
rs2971544	IQCB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118979600-118980200	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr3:118979600-118980200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:118979800-118980200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:118979800-118980200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:118979800-118980200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:118979800-118980200	Enhancers	iPS-15b 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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