Variant report

Variant	rs6808653
Chromosome Location	chr3:68052893-68052894
allele	A/G
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:12)

rs_ID	r²[population]
rs1349005	0.91[JPT][hapmap]
rs1374837	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs4572789	0.91[JPT][hapmap]
rs4856812	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs4856813	0.91[JPT][hapmap]
rs6792324	0.81[CHB][hapmap]
rs7429717	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs7431177	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs9812127	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs9818541	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs9857691	0.91[JPT][hapmap]
rs9874728	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1010231	chr3:67894825-68117879	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1013531	chr3:67917771-68070027	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3442201	chr3:67925312-68064610	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3338669	chr3:67925912-68064160	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3395568	chr3:67955462-68064660	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv876924	chr3:67978367-68063259	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6808653	LRIG1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68048000-68054200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:68048800-68053400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:68051200-68053200	Weak transcription	Aorta	Aorta
4	chr3:68052600-68053000	Enhancers	Fetal Brain Male	brain
5	chr3:68052800-68055400	Active TSS	Fetal Brain Female	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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