Variant report

Variant	rs61602523
Chromosome Location	chr21:46239447-46239448
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46237200-46240136	K562	blood:	n/a	n/a
2	POLR2A	chr21:46236589-46239537	GM12878	blood:	n/a	n/a
3	SETDB1	chr21:46238989-46240079	U2OS	brain:	n/a	chr21:46239232-46239256
4	POLR2A	chr21:46239436-46239606	HepG2	liver:	n/a	n/a
5	POLR2A	chr21:46239212-46239627	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr21:46236599-46239893	K562	blood:	n/a	n/a
7	SETDB1	chr21:46238001-46240087	K562	blood:	n/a	chr21:46239232-46239256
8	CBX3	chr21:46239394-46239806	K562	blood:	n/a	n/a
9	CBX3	chr21:46239328-46239685	K562	blood:	n/a	n/a
10	POLR2A	chr21:46239330-46239488	GM12878	blood:	n/a	n/a
11	POLR2A	chr21:46237296-46239463	K562	blood:	n/a	n/a
12	HEY1	chr21:46238848-46239721	K562	blood:	n/a	n/a
13	KAP1	chr21:46239238-46239878	HEK293	kidney:	n/a	n/a
14	POLR2A	chr21:46238890-46239650	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr21:46236149-46239701	GM12878	blood:	n/a	n/a
16	POLR2A	chr21:46236937-46240089	HepG2	liver:	n/a	n/a
17	POLR2A	chr21:46239364-46239686	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr21:46236230-46240188	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46231216..46239677-chr21:46289090..46295542,14	K562	blood:
2	chr21:46232702..46239829-chr21:46289967..46296620,21	MCF-7	breast:
3	chr21:46231904..46241990-chr21:46492035..46500735,28	K562	blood:
4	chr21:46235459..46240790-chr21:46329963..46334235,7	MCF-7	breast:
5	chr21:45298008..45300010-chr21:46238849..46240379,2	K562	blood:
6	chr21:46231789..46243695-chr21:46286819..46295664,23	MCF-7	breast:
7	chr21:46233435..46239577-chr21:46329843..46334353,8	MCF-7	breast:
8	chr21:46234752..46239628-chr21:46345760..46349592,8	MCF-7	breast:
9	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
10	chr21:46238172..46240580-chr21:46333314..46335686,2	K562	blood:
11	chr21:46236285..46239693-chr21:46357237..46360614,5	K562	blood:
12	chr21:46231513..46241255-chr21:46492035..46497390,26	K562	blood:

No data

No data

No data

Variant related genes	Relation type
SUMO3	TF binding region
ENSG00000235374	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000183255	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11911014	0.81[AMR][1000 genomes]
rs11911580	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11911583	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13433443	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1555002	1.00[ASN][1000 genomes]
rs1555003	1.00[ASN][1000 genomes]
rs57205597	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60685574	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9975401	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9975507	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975777	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979741	0.89[AFR][1000 genomes]
rs9981327	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9984211	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
11	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv913966	chr21:46229393-46261390	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46238600-46239800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:46238600-46240200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:46238800-46239600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr21:46238800-46239600	ZNF genes & repeats	Fetal Intestine Small	intestine
5	chr21:46238800-46239800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr21:46238800-46239800	ZNF genes & repeats	Placenta	Placenta
7	chr21:46238800-46240000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr21:46238800-46240200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr21:46238800-46241000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr21:46239000-46239600	Enhancers	Spleen	Spleen
11	chr21:46239000-46239800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr21:46239000-46240000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr21:46239000-46240200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr21:46239200-46239800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr21:46239200-46240000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
16	chr21:46239400-46240000	ZNF genes & repeats	Thymus	Thymus

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dbSNP/dbVar ID: rs12345 /nsv7879
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