Variant report

Variant	rs11127757
Chromosome Location	chr3:82043062-82043063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs11127754	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127758	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11916839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11917041	0.93[ASN][1000 genomes]
rs11917347	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11918223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919912	0.88[EUR][1000 genomes]
rs11922298	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11929553	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12630225	0.88[EUR][1000 genomes]
rs13059531	0.88[EUR][1000 genomes]
rs13088518	0.82[EUR][1000 genomes]
rs13314987	0.93[EUR][1000 genomes]
rs13321907	0.93[EUR][1000 genomes]
rs13434355	0.93[ASN][1000 genomes]
rs1534668	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17019551	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1919559	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1919565	0.93[ASN][1000 genomes]
rs1919566	0.93[ASN][1000 genomes]
rs2068210	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2068211	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2141489	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2178315	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2178316	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28393435	0.93[ASN][1000 genomes]
rs28455989	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28475537	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28536106	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28561953	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28564625	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28683026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4521254	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60509851	0.93[EUR][1000 genomes]
rs60782263	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61543943	0.89[ASN][1000 genomes]
rs61679258	0.93[ASN][1000 genomes]
rs62265731	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62265755	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62265756	0.88[EUR][1000 genomes]
rs62265757	0.95[EUR][1000 genomes]
rs62268572	0.95[EUR][1000 genomes]
rs6419747	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6548789	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6548790	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6548793	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6548794	0.93[ASN][1000 genomes]
rs66870475	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6763269	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6767358	0.95[EUR][1000 genomes]
rs6769852	0.93[EUR][1000 genomes]
rs6773980	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774064	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774157	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6776655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6778325	0.93[ASN][1000 genomes]
rs6778814	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781140	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792426	0.93[ASN][1000 genomes]
rs6793519	0.93[ASN][1000 genomes]
rs6804280	0.82[ASN][1000 genomes]
rs6805116	0.95[EUR][1000 genomes]
rs7611244	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7611492	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7612452	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7614689	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7615354	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7619146	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622355	0.95[EUR][1000 genomes]
rs7623648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634781	0.90[EUR][1000 genomes]
rs7635092	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639020	0.93[ASN][1000 genomes]
rs7639102	0.89[ASN][1000 genomes]
rs7639908	0.93[ASN][1000 genomes]
rs9309885	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9811625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812010	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9812960	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814587	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9815442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816690	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9817048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819290	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9820525	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820687	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821368	0.95[EUR][1000 genomes]
rs9821506	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821800	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9822483	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832377	0.95[EUR][1000 genomes]
rs9834983	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9836048	0.95[EUR][1000 genomes]
rs9838997	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9840948	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9843444	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9845227	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848134	0.88[EUR][1000 genomes]
rs9849917	0.93[ASN][1000 genomes]
rs9851363	0.88[EUR][1000 genomes]
rs9853043	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9857313	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9857742	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9857763	0.85[ASN][1000 genomes]
rs9858684	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9859766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863450	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9866029	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9866312	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9866476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867563	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9868174	0.93[ASN][1000 genomes]
rs9868182	0.90[EUR][1000 genomes]
rs9869419	0.95[EUR][1000 genomes]
rs9869718	0.93[EUR][1000 genomes]
rs9872972	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9873073	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9875359	0.95[EUR][1000 genomes]
rs9876062	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9876340	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9878115	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9878768	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9882486	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9882687	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9883163	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752870	chr3:82014410-82050310	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11127757	SH2D2A	trans	brain	seeQTL
rs11127757	CRX	trans	brain	seeQTL
rs11127757	DEFB119	trans	brain	seeQTL
rs11127757	DDC	trans	brain	seeQTL
rs11127757	PDE6H	trans	brain	seeQTL
rs11127757	GUCA1C	trans	brain	seeQTL
rs11127757	GSG1	trans	brain	seeQTL
rs11127757	SLC5A7	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:82039400-82046000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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