Variant report

Variant	rs10490261
Chromosome Location	chr2:40917564-40917565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1003616	0.87[EUR][1000 genomes]
rs1003617	0.87[EUR][1000 genomes]
rs10048831	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009356	0.85[CEU][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs10490260	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124753	0.87[EUR][1000 genomes]
rs1116005	0.82[AFR][1000 genomes]
rs12463635	0.87[EUR][1000 genomes]
rs12466363	0.87[EUR][1000 genomes]
rs12466428	0.94[AFR][1000 genomes]
rs12466466	0.87[EUR][1000 genomes]
rs12469295	0.95[AFR][1000 genomes]
rs12474038	0.81[EUR][1000 genomes]
rs12474457	0.81[EUR][1000 genomes]
rs12474560	0.81[EUR][1000 genomes]
rs12474649	0.93[EUR][1000 genomes]
rs12477533	0.88[EUR][1000 genomes]
rs12712708	0.87[CHD][hapmap]
rs13016866	0.82[JPT][hapmap]
rs13414829	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs13422403	0.90[EUR][1000 genomes]
rs17026449	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17026478	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17026493	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026498	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026547	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17039019	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17479653	0.92[EUR][1000 genomes]
rs1861302	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1861303	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2024437	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs2192819	0.83[AFR][1000 genomes]
rs2192820	0.85[AFR][1000 genomes]
rs2216044	0.81[EUR][1000 genomes]
rs2216045	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2888698	0.82[EUR][1000 genomes]
rs34359856	0.81[EUR][1000 genomes]
rs3851315	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3851316	0.88[EUR][1000 genomes]
rs3851317	0.82[CEU][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs42786	0.82[EUR][1000 genomes]
rs42789	0.83[EUR][1000 genomes]
rs4387847	0.83[EUR][1000 genomes]
rs4952640	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55670471	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55690670	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs55772101	0.81[EUR][1000 genomes]
rs55878022	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56121667	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56321003	0.94[EUR][1000 genomes]
rs56336113	0.81[EUR][1000 genomes]
rs56342806	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs57243979	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57625048	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57950795	0.86[EUR][1000 genomes]
rs62139477	0.93[EUR][1000 genomes]
rs62139487	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62139540	0.96[AFR][1000 genomes]
rs6714526	0.80[EUR][1000 genomes]
rs6720960	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6721900	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6755751	0.87[EUR][1000 genomes]
rs7563703	0.84[CEU][hapmap]
rs7563807	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584710	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs888021	0.93[EUR][1000 genomes]
rs983123	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873924	chr2:40835285-40926138	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873931	chr2:40869165-40966719	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv456441	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv581514	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv456452	chr2:40890416-40989061	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv581515	chr2:40890416-40989061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv3584751	chr2:40916853-40952073	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10490261	TMEM178	cis	parietal	SCAN
rs10490261	FEZ2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40913600-40920200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:40915200-40917600	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:40917200-40917800	Enhancers	Aorta	Aorta
4	chr2:40917400-40917600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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