Variant report

Variant	rs13049379
Chromosome Location	chr21:45900553-45900554
allele	G/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	chr21:45900222-45900865	Hela-S3	cervix:	n/a	n/a
2	TBP	chr21:45900238-45900645	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr21:45900333-45900918	Hela-S3	cervix:	n/a	n/a
4	RCOR1	chr21:45900184-45900699	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr21:45900217-45900839	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr21:45900217-45900899	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr21:45900265-45900620	Hela-S3	cervix:	n/a	n/a
8	TCF7L2	chr21:45900322-45900688	Hela-S3	cervix:	n/a	n/a
9	ZKSCAN1	chr21:45900262-45900563	Hela-S3	cervix:	n/a	n/a
10	SMC3	chr21:45900230-45900623	Hela-S3	cervix:	n/a	chr21:45900334-45900344
11	GTF2F1	chr21:45900262-45900678	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr21:45900102-45900859	Hela-S3	cervix:	n/a	n/a
13	MYC	chr21:45900182-45900945	Hela-S3	cervix:	n/a	n/a
14	RFX5	chr21:45900351-45901017	Hela-S3	cervix:	n/a	n/a
15	MAX	chr21:45900170-45900934	Hela-S3	cervix:	n/a	n/a
16	ELK1	chr21:45900251-45900587	Hela-S3	cervix:	n/a	n/a
17	GATA3	chr21:45900095-45900757	MCF-7	breast:	n/a	n/a
18	CHD2	chr21:45900201-45900833	Hela-S3	cervix:	n/a	n/a
19	BRCA1	chr21:45900162-45900622	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45898990..45900999-chr21:45903526..45905351,2	MCF-7	breast:
2	chr21:45875711..45878548-chr21:45899746..45901735,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228709	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12627610	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13050591	1.00[EUR][1000 genomes]
rs13051665	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838568	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2838569	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838570	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838571	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838572	0.90[ASN][1000 genomes]
rs34672935	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7276430	0.94[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

No data

Chromatin state (count:15 , 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	chr21:45898800-45902000	Weak transcription	Fetal Intestine Small	intestine
5	chr21:45898800-45902000	Weak transcription	Placenta	Placenta
6	chr21:45898800-45902400	Weak transcription	Pancreas	Pancrea
7	chr21:45898800-45905400	Weak transcription	Fetal Brain Female	brain
8	chr21:45898800-45906200	Weak transcription	Spleen	Spleen
9	chr21:45899000-45903800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr21:45899800-45901000	Enhancers	Liver	Liver
11	chr21:45900000-45900600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr21:45900000-45900800	Flanking Active TSS	HepG2	liver
13	chr21:45900000-45901000	Flanking Active TSS	Hela-S3	cervix
14	chr21:45900200-45900800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr21:45900200-45900800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links