Variant report

Variant	rs2838433
Chromosome Location	chr21:45333865-45333866
allele	A/G
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	TCF7L2	chr21:45333718-45334256	HEK293	kidney:	n/a	n/a
2	ATF1	chr21:45333799-45334132	K562	blood:	n/a	n/a
3	MAX	chr21:45333784-45334173	K562	blood:	n/a	chr21:45334069-45334079
4	CREB1	chr21:45333739-45334116	GM12878	blood:	n/a	n/a
5	CBX3	chr21:45333340-45334152	K562	blood:	n/a	n/a
6	CREB1	chr21:45333732-45334238	K562	blood:	n/a	n/a
7	MEF2A	chr21:45333777-45334120	K562	blood:	n/a	chr21:45333910-45333925
8	NR2F2	chr21:45333727-45334124	K562	blood:	n/a	n/a
9	NR2F2	chr21:45333690-45334236	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45317953..45320008-chr21:45333800..45335769,2	K562	blood:
2	chr21:45322017..45325690-chr21:45333512..45336768,4	MCF-7	breast:
3	chr21:45284170..45285770-chr21:45332539..45334040,2	K562	blood:

Variant related genes	Relation type
AGPAT3	TF binding region
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11700575	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070546	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs2070548	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2070549	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2838434	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788075	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788082	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4819337	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4819338	0.88[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4819339	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4819341	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58565118	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59355960	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60216010	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60316193	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7278539	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73226931	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9647250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975713	0.91[ASN][1000 genomes]
rs9983066	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	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
4	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1066284	chr21:45249549-45343314	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv19383	chr21:45326239-45334057	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838433	C21orf88	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45314800-45336000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr21:45316600-45336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr21:45324000-45336000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr21:45324600-45337200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr21:45326800-45336600	Weak transcription	Colonic Mucosa	Colon
6	chr21:45327200-45336000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr21:45327200-45336600	Weak transcription	Ovary	ovary
8	chr21:45327400-45336000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr21:45328400-45336000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr21:45328800-45334200	Enhancers	Fetal Intestine Large	intestine
11	chr21:45328800-45336400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr21:45329000-45336000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr21:45329800-45334200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr21:45330200-45336600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:45331400-45334200	ZNF genes & repeats	GM12878-XiMat	blood
16	chr21:45331600-45334400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr21:45331600-45336400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr21:45331800-45337200	Weak transcription	Stomach Mucosa	stomach
19	chr21:45332000-45334200	Enhancers	Liver	Liver
20	chr21:45332000-45336400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:45332000-45337400	Weak transcription	Small Intestine	intestine
22	chr21:45332200-45336000	Weak transcription	Brain Substantia Nigra	brain
23	chr21:45332200-45336200	Weak transcription	Fetal Heart	heart
24	chr21:45332200-45336600	Weak transcription	Pancreas	Pancrea
25	chr21:45332200-45336800	Weak transcription	Gastric	stomach
26	chr21:45332400-45334200	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr21:45332400-45336800	Weak transcription	Lung	lung
28	chr21:45332400-45336800	Weak transcription	Spleen	Spleen
29	chr21:45332600-45336000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr21:45332600-45336600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr21:45332600-45336600	Weak transcription	Right Ventricle	heart
32	chr21:45332800-45336200	Weak transcription	Fetal Lung	lung
33	chr21:45332800-45336400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr21:45332800-45336800	Weak transcription	Esophagus	oesophagus
35	chr21:45332800-45340000	Weak transcription	Fetal Kidney	kidney
36	chr21:45333000-45334000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:45333000-45335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr21:45333000-45336000	Weak transcription	Primary T cells from cord blood	blood
39	chr21:45333000-45336000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr21:45333000-45336000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr21:45333000-45336000	Weak transcription	Osteobl	bone
42	chr21:45333000-45336200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr21:45333000-45336400	Weak transcription	Thymus	Thymus
44	chr21:45333000-45336600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr21:45333000-45336600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr21:45333000-45336800	Weak transcription	Colon Smooth Muscle	Colon
47	chr21:45333000-45337000	Weak transcription	Brain Germinal Matrix	brain
48	chr21:45333000-45337200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr21:45333000-45341000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr21:45333000-45341200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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