Variant report

Variant	rs2838572
Chromosome Location	chr21:45902320-45902321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr21:45902320-45904197	HepG2	liver:	n/a	n/a
2	POLR2A	chr21:45902243-45905465	HepG2	liver:	n/a	n/a
3	SP1	chr21:45902241-45903085	HepG2	liver:	n/a	n/a
4	CTCF	chr21:45902320-45902470	K562	blood:	n/a	n/a
5	ARID3A	chr21:45902209-45902897	HepG2	liver:	n/a	n/a
6	RXRA	chr21:45902234-45902817	HepG2	liver:	n/a	n/a
7	MAFK	chr21:45902309-45902947	HepG2	liver:	n/a	n/a
8	MYBL2	chr21:45902266-45903677	HepG2	liver:	n/a	n/a
9	RCOR1	chr21:45902260-45902895	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45902107..45904148-chr21:45905322..45907862,2	K562	blood:
2	chr21:45900988..45903859-chr21:46349141..46351418,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228709	TF binding region
ENSG00000273027	Chromatin interaction
ENSG00000228709	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12627610	0.86[ASW][hapmap];0.82[CEU][hapmap];0.88[MEX][hapmap]
rs13048314	0.98[EUR][1000 genomes]
rs13049379	0.90[ASN][1000 genomes]
rs2838568	0.86[ASW][hapmap];0.82[CHB][hapmap];0.88[MEX][hapmap]
rs2838569	0.86[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[MEX][hapmap]
rs2838571	0.82[CEU][hapmap];0.88[MEX][hapmap]
rs2838573	0.98[EUR][1000 genomes]
rs4818927	0.99[EUR][1000 genomes]
rs9306105	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
3	esv3361489	chr21:45669073-46013747	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
4	nsv913918	chr21:45697755-45941566	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv1058359	chr21:45724055-45941566	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
6	nsv1065203	chr21:45731690-45941566	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv544473	chr21:45731690-45941566	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv913942	chr21:45740823-45941566	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv913943	chr21:45740823-46031810	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv1067264	chr21:45757599-45941566	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv544474	chr21:45757599-45941566	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv913944	chr21:45757905-45941566	Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
13	nsv1058534	chr21:45812976-45916560	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv587801	chr21:45832912-45916560	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv913946	chr21:45838632-46031810	Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
16	nsv913948	chr21:45860912-46031810	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	nsv834109	chr21:45869352-45916560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv1056424	chr21:45894901-46031810	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
19	nsv544475	chr21:45894901-46031810	Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv1055163	chr21:45895663-46031810	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2838572	TRAPPC10	cis	cerebellum	SCAN
rs2838572	CSTB	cis	cerebellum	SCAN
rs2838572	PWP2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45881800-45911800	Weak transcription	Right Atrium	heart
2	chr21:45896200-45905400	Weak transcription	Brain Germinal Matrix	brain
3	chr21:45898600-45905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr21:45898800-45902400	Weak transcription	Pancreas	Pancrea
5	chr21:45898800-45905400	Weak transcription	Fetal Brain Female	brain
6	chr21:45898800-45906200	Weak transcription	Spleen	Spleen
7	chr21:45899000-45903800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr21:45900800-45902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:45900800-45902800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:45900800-45905000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr21:45901000-45902600	Enhancers	Hela-S3	cervix
12	chr21:45901000-45916000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr21:45902000-45902400	Enhancers	Liver	Liver
14	chr21:45902000-45902600	Enhancers	Fetal Intestine Small	intestine
15	chr21:45902000-45902600	Flanking Active TSS	HepG2	liver
16	chr21:45902000-45903000	Enhancers	Fetal Intestine Large	intestine
17	chr21:45902000-45903200	Enhancers	Placenta	Placenta
18	chr21:45902000-45903600	Enhancers	Stomach Mucosa	stomach
19	chr21:45902000-45904400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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