Variant report

Variant	rs2083868
Chromosome Location	chr1:75922251-75922252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10518500	0.94[CEU][hapmap]
rs11163461	0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs11163490	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11163493	0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs11163496	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11804097	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs11806471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11809429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11811008	0.84[EUR][1000 genomes]
rs12402118	0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs1249777	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1249783	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1249794	0.82[CHD][hapmap]
rs1249796	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1249797	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1249807	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1249823	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1343519	0.83[CHD][hapmap]
rs1443846	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17096860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17096877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs17584530	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1778454	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1891902	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs211786	0.85[CHB][hapmap]
rs2347215	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2347217	1.00[CHB][hapmap]
rs3845363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588830	0.81[CEU][hapmap]
rs590301	0.81[CEU][hapmap]
rs596515	0.80[CEU][hapmap]
rs598649	0.87[CEU][hapmap]
rs604745	0.81[CEU][hapmap]
rs617196	0.81[CEU][hapmap]
rs625357	0.81[CEU][hapmap]
rs629615	0.81[CEU][hapmap]
rs635184	0.81[CEU][hapmap]
rs639028	0.80[CEU][hapmap]
rs642923	0.81[CEU][hapmap]
rs663620	0.81[CEU][hapmap]
rs664268	0.81[CEU][hapmap]
rs6657734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6676696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs671919	0.87[CEU][hapmap]
rs675962	0.80[CEU][hapmap]
rs694025	0.81[CEU][hapmap]
rs74089241	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1011915	chr1:75879330-75934553	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv546581	chr1:75897055-75937429	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3359779	chr1:75914980-75939472	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2083868	LHX8	cis	parietal	SCAN
rs2083868	SLC44A5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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

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