Variant report

Variant	rs2838617
Chromosome Location	chr21:46077812-46077813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10854463	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11701054	0.83[AFR][1000 genomes]
rs12106369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12482870	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13051885	0.86[JPT][hapmap]
rs1883039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1883041	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073437	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2210284	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2225433	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2256361	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2256490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256496	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2329837	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2329838	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2329839	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2329840	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2329841	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2329842	0.91[ASN][1000 genomes]
rs2329843	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838601	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2838602	0.95[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2838610	0.95[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2838611	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2838612	0.82[JPT][hapmap]
rs2838614	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838618	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838619	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2838623	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838634	0.90[CHB][hapmap]
rs28542851	0.82[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs34979768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3944594	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3966427	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4050979	0.86[JPT][hapmap]
rs463217	0.95[CEU][hapmap]
rs4818728	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818947	0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4818950	0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs4818952	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4818953	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68065001	0.86[AFR][1000 genomes]
rs7275203	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275666	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7276421	0.95[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7277758	0.96[ASN][1000 genomes]
rs7280471	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7282421	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7509675	0.82[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs762431	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs762433	0.92[EUR][1000 genomes]
rs8126553	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8129802	0.91[JPT][hapmap]
rs8132337	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8132352	0.81[JPT][hapmap]
rs926193	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9284507	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs9306111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9974195	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983892	0.87[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9984726	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065798	chr21:45941000-46097463	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv869108	chr21:45941000-46097463	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv544476	chr21:45941000-46097463	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv913950	chr21:45985068-46097463	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2838617	UMODL1	cis	cerebellum	SCAN
rs2838617	C21orf70	cis	parietal	SCAN
rs2838617	KRTAP12-2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46073600-46079800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr21:46073600-46080200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr21:46076800-46078600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:46076800-46078800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr21:46076800-46080000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr21:46077000-46078200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr21:46077000-46079400	Enhancers	Dnd41	blood
8	chr21:46077200-46079000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr21:46077200-46080400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr21:46077400-46078200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr21:46077400-46078200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr21:46077400-46080200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr21:46077600-46078600	Enhancers	Spleen	Spleen
14	chr21:46077600-46078800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr21:46077800-46078000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr21:46077800-46078000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:46077800-46078000	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr21:46077800-46078200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr21:46077800-46078200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:46077800-46078200	Weak transcription	Primary T cells from cord blood	blood
21	chr21:46077800-46078200	Enhancers	Placenta	Placenta
22	chr21:46077800-46078400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr21:46077800-46078400	Enhancers	Fetal Brain Male	brain
24	chr21:46077800-46078600	Enhancers	Esophagus	oesophagus
25	chr21:46077800-46080200	Enhancers	Primary T helper cells PMA-I stimulated	--

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