Variant report

Variant	rs2090126
Chromosome Location	chr10:50206125-50206126
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10735228	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10745290	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs10776660	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs10857430	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs10857431	0.81[EUR][1000 genomes]
rs11101573	0.89[CHB][hapmap]
rs12413832	0.81[CEU][hapmap]
rs1877799	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1877800	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1913516	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs1913528	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2090127	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2137909	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs2245379	0.92[ASN][1000 genomes]
rs2245392	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2249657	0.86[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2249659	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2249662	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2252811	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2264553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271565	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs2292584	0.82[CEU][hapmap]
rs2292585	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2457466	0.82[TSI][hapmap]
rs2458671	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2458675	0.86[ASN][1000 genomes]
rs2663028	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs2663067	0.94[JPT][hapmap]
rs2663068	0.94[JPT][hapmap]
rs2889709	0.88[JPT][hapmap]
rs4614357	0.81[CEU][hapmap]
rs4838433	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838663	0.82[ASN][1000 genomes]
rs6537586	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs6537587	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap]
rs7083751	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs7086917	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap]
rs7091429	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs7093656	0.82[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap]
rs7913932	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	esv3502799	chr10:50196746-50208344	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3502797	chr10:50197246-50208144	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv6620	chr10:50197344-50224635	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3502798	chr10:50197531-50207624	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3314886	chr10:50197812-50207300	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3314897	chr10:50197842-50207294	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3502795	chr10:50197861-50207300	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3502801	chr10:50197869-50207271	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3502800	chr10:50197875-50207222	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv3502802	chr10:50197909-50207239	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3314908	chr10:50197969-50207188	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv3502803	chr10:50197969-50207188	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv3520105	chr10:50204729-50207237	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
16	esv3520106	chr10:50204729-50207237	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
17	esv16567	chr10:50205831-50206997	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2090126	CSTF2T	cis	parietal	SCAN
rs2090126	WDFY4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50205000-50206600	Weak transcription	Fetal Intestine Large	intestine
2	chr10:50205200-50206200	Weak transcription	Fetal Intestine Small	intestine

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