Variant report

Variant	rs10439299
Chromosome Location	chr2:180083187-180083188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10170520	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10174774	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10186198	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10192426	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10205390	0.81[AFR][1000 genomes]
rs10205999	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10930858	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1158872	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11884516	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11894870	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11898291	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12997314	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13026497	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13383965	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13391602	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13418701	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374378	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1907421	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1979053	0.81[EUR][1000 genomes]
rs2008989	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2008999	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2289992	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2847	0.84[EUR][1000 genomes]
rs4585064	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6433757	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6433760	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433761	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433764	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433769	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6707081	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6734121	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6736098	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742739	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6743405	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6756326	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7562730	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7579536	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7585600	0.88[EUR][1000 genomes]
rs7608236	0.83[AMR][1000 genomes]
rs7608882	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9288022	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3061	chr2:180057194-180095718	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv14990	chr2:180060110-180083212	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv821830	chr2:180060110-180083212	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2427556	chr2:180060320-180083338	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv436303	chr2:180065337-180083364	Enhancers ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv583774	chr2:180068214-180083591	ZNF genes & repeats Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv1840933	chr2:180068214-180089983	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv583840	chr2:180069686-180083591	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3341806	chr2:180070495-180093344	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv583862	chr2:180070574-180083591	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv508185	chr2:180070760-180085648	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv583865	chr2:180072586-180088968	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10439299	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180067600-180097600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:180067600-180104600	Weak transcription	Fetal Kidney	kidney
3	chr2:180068000-180103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:180068400-180092800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:180072400-180090400	Weak transcription	Pancreas	Pancrea
6	chr2:180077600-180086400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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