Variant report

Variant	rs9977480
Chromosome Location	chr21:46224456-46224457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46224333-46224591	GM12891	blood:	n/a	n/a
2	POLR2A	chr21:46224273-46225112	K562	blood:	n/a	n/a
3	POLR2A	chr21:46223597-46225876	HEK293	kidney:	n/a	n/a
4	POLR2A	chr21:46220877-46225649	K562	blood:	n/a	n/a
5	POLR2A	chr21:46220980-46225308	K562	blood:	n/a	n/a
6	POLR2A	chr21:46221338-46225872	GM12878	blood:	n/a	n/a
7	POLR2A	chr21:46224365-46224557	GM12878	blood:	n/a	n/a
8	POLR2A	chr21:46223465-46225324	HCT-116	colon:	n/a	n/a
9	POLR2A	chr21:46220710-46226000	K562	blood:	n/a	n/a
10	POLR2A	chr21:46220981-46225932	K562	blood:	n/a	n/a
11	POLR2A	chr21:46221323-46224680	GM12892	blood:	n/a	n/a
12	POLR2A	chr21:46224230-46224599	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr21:46223987-46224485	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr21:46220458-46225731	K562	blood:	n/a	n/a
15	POLR2A	chr21:46223272-46225438	GM12892	blood:	n/a	n/a
16	POLR2A	chr21:46224055-46226000	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr21:46222035-46224585	GM12892	blood:	n/a	n/a
18	POLR2A	chr21:46223810-46225354	A549	lung:	n/a	n/a
19	POLR2A	chr21:46224306-46224550	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr21:46221076-46225970	GM12878	blood:	n/a	n/a
21	POLR2A	chr21:46222351-46225533	GM12878	blood:	n/a	n/a
22	POLR2A	chr21:46221326-46226084	HepG2	liver:	n/a	n/a
23	POLR2A	chr21:46223661-46225367	HepG2	liver:	n/a	n/a
24	POLR2A	chr21:46224208-46224494	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr21:46224046-46225500	MCF-7	breast:	n/a	n/a
26	POLR2A	chr21:46221340-46225636	GM12892	blood:	n/a	n/a
27	POLR2A	chr21:46224342-46224521	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr21:46220647-46225708	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr21:46220865-46226037	GM12891	blood:	n/a	n/a
30	POLR2A	chr21:46221412-46224646	GM12891	blood:	n/a	n/a
31	POLR2A	chr21:46223376-46225822	Raji	blood:	n/a	n/a
32	POLR2A	chr21:46224318-46224518	GM12878	blood:	n/a	n/a
33	POLR2A	chr21:46224290-46224655	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr21:46223566-46225559	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr21:46224367-46224560	GM12878	blood:	n/a	n/a
36	POLR2A	chr21:46222085-46225519	GM12891	blood:	n/a	n/a
37	POLR2A	chr21:46224326-46224569	Hela-S3	cervix:	n/a	n/a
38	USF2	chr21:46224378-46225347	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr21:46221550-46227421	K562	blood:	n/a	n/a
40	POLR2A	chr21:46224348-46224534	HepG2	liver:	n/a	n/a
41	POLR2A	chr21:46222376-46225739	HepG2	liver:	n/a	n/a
42	POLR2A	chr21:46221486-46225982	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr21:46221077-46225480	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr21:46223316-46224648	K562	blood:	n/a	n/a
45	POLR2A	chr21:46224345-46225590	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr21:46224167-46225495	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr21:46223983-46224494	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46223596..46225546-chr21:46364000..46366683,2	MCF-7	breast:
2	chr21:46223675..46225793-chr21:46292285..46293975,2	MCF-7	breast:
3	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
4	chr21:46224269..46228564-chr21:46290759..46294027,4	K562	blood:
5	chr21:46222712..46224808-chr21:46281066..46282729,2	MCF-7	breast:
6	chr21:46223417..46225728-chr21:46304439..46306955,2	K562	blood:
7	chr21:46220930..46225769-chr21:46292170..46294469,5	K562	blood:
8	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
9	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KRTAP10-12-1	chr21:46223662-46224632	XLOC_013973

No data

Variant related genes	Relation type
UBE2G2	TF binding region
ENSG00000273027	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000183250	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1051331	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217834	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17289578	0.80[EUR][1000 genomes]
rs17289745	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2017089	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2838690	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838691	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838692	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728356	0.85[EUR][1000 genomes]
rs8645	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873301	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9977684	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9984357	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv459298	chr21:46223847-46277968	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv587813	chr21:46223847-46277968	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv913963	chr21:46223847-46277968	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
9	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46222400-46236400	Weak transcription	Small Intestine	intestine
2	chr21:46222600-46224600	Weak transcription	Brain Angular Gyrus	brain
3	chr21:46222600-46224800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:46222600-46224800	Weak transcription	Aorta	Aorta
5	chr21:46222600-46224800	Weak transcription	Left Ventricle	heart
6	chr21:46222600-46224800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr21:46222600-46225000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr21:46222600-46226200	Weak transcription	Esophagus	oesophagus
9	chr21:46222600-46226800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr21:46222600-46234800	Weak transcription	Right Atrium	heart
11	chr21:46222600-46236400	Weak transcription	Stomach Mucosa	stomach
12	chr21:46222600-46237200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr21:46222800-46224600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr21:46222800-46224800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr21:46222800-46224800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr21:46222800-46224800	Weak transcription	Brain Substantia Nigra	brain
17	chr21:46222800-46224800	Weak transcription	Fetal Brain Female	brain
18	chr21:46222800-46224800	Weak transcription	Ovary	ovary
19	chr21:46222800-46224800	Weak transcription	Pancreas	Pancrea
20	chr21:46222800-46224800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:46222800-46224800	Weak transcription	Thymus	Thymus
22	chr21:46222800-46224800	Weak transcription	NHDF-Ad	bronchial
23	chr21:46222800-46225000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr21:46222800-46225000	Weak transcription	Brain Hippocampus Middle	brain
25	chr21:46222800-46225200	Weak transcription	Fetal Brain Male	brain
26	chr21:46222800-46225200	Weak transcription	Fetal Kidney	kidney
27	chr21:46222800-46225400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr21:46222800-46226400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr21:46222800-46226400	Weak transcription	Gastric	stomach
30	chr21:46222800-46226600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr21:46222800-46236400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr21:46222800-46237200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr21:46223000-46224600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr21:46223000-46224600	Weak transcription	Adipose Nuclei	Adipose
35	chr21:46223000-46224600	Weak transcription	GM12878-XiMat	blood
36	chr21:46223000-46224800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr21:46223000-46224800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr21:46223000-46224800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr21:46223000-46224800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr21:46223000-46224800	Weak transcription	Brain Germinal Matrix	brain
41	chr21:46223000-46224800	Weak transcription	Colonic Mucosa	Colon
42	chr21:46223000-46224800	Weak transcription	Fetal Lung	lung
43	chr21:46223000-46224800	Weak transcription	Fetal Thymus	thymus
44	chr21:46223000-46224800	Weak transcription	Lung	lung
45	chr21:46223000-46224800	Weak transcription	Spleen	Spleen
46	chr21:46223000-46225000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr21:46223000-46225200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr21:46223000-46225200	Weak transcription	Right Ventricle	heart
49	chr21:46223000-46225200	Weak transcription	NH-A	brain
50	chr21:46223000-46225800	Weak transcription	Placenta Amnion	Placenta Amnion

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