Variant report

Variant	rs2838616
Chromosome Location	chr21:46077122-46077123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12481809	0.82[ASN][1000 genomes]
rs12482041	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12483730	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12626853	0.84[LWK][hapmap]
rs2838615	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838626	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2838630	0.86[CHB][hapmap];0.92[CHD][hapmap]
rs2838645	0.85[CHD][hapmap]
rs2838649	0.85[CHD][hapmap]
rs28796990	0.84[ASN][1000 genomes]
rs4818729	0.84[ASN][1000 genomes]
rs55914221	0.82[ASN][1000 genomes]
rs55957933	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7283084	0.86[CHB][hapmap];0.92[CHD][hapmap]
rs7283406	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9637188	0.86[CHB][hapmap]
rs9974365	0.82[ASN][1000 genomes]
rs9979168	0.84[ASN][1000 genomes]
rs9980087	0.85[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838616	PDXK	cis	cerebellum	SCAN
rs2838616	UMODL1	cis	cerebellum	SCAN

Chromatin state (count:17 , 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	chr21:46075400-46077200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
4	chr21:46076200-46077600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr21:46076600-46077400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr21:46076600-46077400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr21:46076600-46077800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:46076800-46077200	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr21:46076800-46077400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr21:46076800-46077400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr21:46076800-46077600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr21:46076800-46078600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr21:46076800-46078800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr21:46076800-46080000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr21:46077000-46077200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
16	chr21:46077000-46078200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr21:46077000-46079400	Enhancers	Dnd41	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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