Variant report

Variant	rs11088972
Chromosome Location	chr21:46360757-46360758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr21:46359328-46361037	IMR90	lung:	n/a	n/a
2	MXI1	chr21:46358871-46361050	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr21:46360680-46360830	AG10803	skin:	n/a	n/a
4	JUN	chr21:46358206-46361110	K562	blood:	n/a	chr21:46358894-46358905
5	ZNF384	chr21:46360361-46360800	K562	blood:	n/a	n/a
6	TBP	chr21:46360660-46360847	K562	blood:	n/a	n/a
7	MYC	chr21:46360528-46361127	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr21:46358415-46360873	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr21:46359561-46360798	K562	blood:	n/a	chr21:46360118-46360128
10	MXI1	chr21:46359109-46361016	IMR90	lung:	n/a	n/a
11	POLR2A	chr21:46356473-46360821	MCF10A-Er-Src	breast:	n/a	n/a
12	SIN3AK20	chr21:46359403-46360838	MCF-7	breast:	n/a	n/a
13	GABPA	chr21:46359218-46360799	MCF-7	breast:	n/a	chr21:46359828-46359842

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46348854..46378176-chr21:46489799..46500436,75	K562	blood:
2	chr21:46359964..46363434-chr21:46389610..46392494,4	K562	blood:
3	chr21:46235785..46239443-chr21:46357143..46362674,8	MCF-7	breast:
4	chr21:46291916..46297365-chr21:46358001..46363812,14	MCF-7	breast:
5	chr21:46358715..46360802-chr21:46377914..46380232,3	K562	blood:
6	chr21:46358799..46362946-chr21:46546409..46551680,5	K562	blood:
7	chr21:46153888..46156616-chr21:46360093..46361664,2	MCF-7	breast:
8	chr21:46353923..46356909-chr21:46357554..46361249,6	K562	blood:
9	chr21:46360355..46363434-chr21:46390613..46392494,3	K562	blood:
10	chr21:46355061..46362857-chr21:46490375..46496482,13	K562	blood:
11	chr21:46236918..46239386-chr21:46357793..46361272,3	K562	blood:
12	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
13	chr21:46220260..46222802-chr21:46358731..46365262,8	MCF-7	breast:

No data

Variant related genes	Relation type
C21orf67	TF binding region
ENSG00000160256	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000272825	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000268856	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10775679	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11088970	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088973	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11701017	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11701173	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11701737	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12106389	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12626600	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13046102	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294169	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838749	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827260	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818745	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818989	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818991	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818992	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818998	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819000	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56122469	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56199687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7277732	0.92[EUR][1000 genomes]
rs7278544	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7278847	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7283236	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9974072	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9974152	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9974593	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9976402	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv913970	chr21:46305175-46487831	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv933240	chr21:46305956-46371518	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv913974	chr21:46306161-46430792	Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv913975	chr21:46306161-46459432	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv913976	chr21:46306161-46487831	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
10	nsv1064518	chr21:46317690-46413159	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv913977	chr21:46335761-46454391	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv913978	chr21:46335761-46466674	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913979	chr21:46335761-46472929	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv913980	chr21:46337565-46454391	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv913981	chr21:46344426-46408790	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv913982	chr21:46344426-46430792	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv913984	chr21:46344426-46435610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv913983	chr21:46344426-46440385	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
19	nsv913985	chr21:46344426-46448142	Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv913986	chr21:46344426-46466674	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv913987	chr21:46344426-46472929	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	nsv913988	chr21:46356816-46408790	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
23	nsv913989	chr21:46356816-46430792	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
24	nsv913990	chr21:46356816-46448142	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
25	nsv913991	chr21:46356816-46472929	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11088972	C21orf69	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46358800-46360800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr21:46358800-46361000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr21:46359000-46361000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr21:46359000-46361000	Active TSS	Fetal Kidney	kidney
5	chr21:46359000-46361200	Active TSS	A549	lung
6	chr21:46359000-46361600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr21:46359000-46361600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr21:46359200-46360800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr21:46359200-46360800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr21:46359200-46360800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr21:46359200-46360800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:46359200-46361000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr21:46359200-46361000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr21:46359200-46361000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr21:46359200-46361200	Active TSS	Psoas Muscle	Psoas
16	chr21:46359200-46361200	Active TSS	GM12878-XiMat	blood
17	chr21:46359200-46361400	Active TSS	Left Ventricle	heart
18	chr21:46359200-46361400	Active TSS	HSMMtube	muscle
19	chr21:46359400-46360800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr21:46359400-46360800	Active TSS	H1 Cell Line	embryonic stem cell
21	chr21:46359400-46360800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr21:46359400-46360800	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr21:46359400-46360800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr21:46359400-46360800	Active TSS	Aorta	Aorta
25	chr21:46359400-46360800	Active TSS	Fetal Intestine Large	intestine
26	chr21:46359400-46360800	Active TSS	Fetal Intestine Small	intestine
27	chr21:46359400-46360800	Active TSS	Fetal Lung	lung
28	chr21:46359400-46360800	Active TSS	K562	blood
29	chr21:46359400-46361000	Active TSS	Brain Germinal Matrix	brain
30	chr21:46359400-46361000	Active TSS	Fetal Brain Male	brain
31	chr21:46359400-46361000	Active TSS	HSMM	muscle
32	chr21:46359400-46361000	Active TSS	NHDF-Ad	bronchial
33	chr21:46359400-46361200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr21:46359400-46361200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr21:46359400-46361200	Active TSS	Fetal Brain Female	brain
36	chr21:46359600-46360800	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr21:46359600-46360800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr21:46359600-46360800	Active TSS	Stomach Mucosa	stomach
39	chr21:46359600-46361000	Active TSS	Fetal Muscle Trunk	muscle
40	chr21:46359600-46361000	Active TSS	Ovary	ovary
41	chr21:46359600-46361000	Active TSS	Right Ventricle	heart
42	chr21:46359600-46361400	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr21:46359600-46361400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr21:46360200-46360800	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr21:46360200-46360800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr21:46360200-46360800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr21:46360200-46361000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr21:46360200-46361000	Bivalent/Poised TSS	HepG2	liver
49	chr21:46360200-46361200	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr21:46360200-46361200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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