Variant report

Variant	rs556962
Chromosome Location	chr6:69503064-69503065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1283949	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16900397	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs2249399	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2250130	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs2585591	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2585595	1.00[EUR][1000 genomes]
rs2585606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2585613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2585615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2746139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802685	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802686	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802695	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2802711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs570708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs578564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv886131	chr6:69480628-69545903	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv886132	chr6:69487204-69610281	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1017659	chr6:69489481-69520127	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3435115	chr6:69502552-69503124	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs556962	FOXG1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69489600-69507000	Weak transcription	Fetal Lung	lung
2	chr6:69500200-69504600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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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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