Variant report

Variant	rs16954126
Chromosome Location	chr16:80872052-80872053
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	CHD2	chr16:80871088-80872288	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr16:80870845-80872356	Hela-S3	cervix:	n/a	n/a
3	EP300	chr16:80870003-80872168	Hela-S3	cervix:	n/a	chr16:80871157-80871170 chr16:80871612-80871626 chr16:80871613-80871627
4	JUND	chr16:80871358-80872064	T-47D	breast:	n/a	n/a
5	RFX5	chr16:80870847-80872367	Hela-S3	cervix:	n/a	chr16:80871252-80871266
6	MYC	chr16:80870664-80872118	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr16:80870345-80872594	Hela-S3	cervix:	n/a	n/a
8	GTF2F1	chr16:80870188-80872239	Hela-S3	cervix:	n/a	n/a
9	JUND	chr16:80871383-80872217	T-47D	breast:	n/a	n/a
10	STAT3	chr16:80870785-80872196	Hela-S3	cervix:	n/a	chr16:80871539-80871547 chr16:80871329-80871337
11	KAP1	chr16:80871394-80872141	U2OS	brain:	n/a	n/a
12	SMC3	chr16:80870876-80872234	Hela-S3	cervix:	n/a	chr16:80871793-80871803
13	STAT1	chr16:80871527-80872280	Hela-S3	cervix:	n/a	chr16:80871539-80871547 chr16:80872029-80872040
14	MAX	chr16:80870740-80872191	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr16:80870801-80872254	Hela-S3	cervix:	n/a	n/a
16	USF2	chr16:80871400-80872170	Hela-S3	cervix:	n/a	n/a
17	EP300	chr16:80871369-80872250	T-47D	breast:	n/a	chr16:80871612-80871626 chr16:80871613-80871627 chr16:80872229-80872239
18	EP300	chr16:80871419-80872075	MCF-7	breast:	n/a	chr16:80871612-80871626 chr16:80871613-80871627
19	NR2F2	chr16:80871496-80872102	MCF-7	breast:	n/a	n/a
20	TCF7L2	chr16:80870644-80872246	Hela-S3	cervix:	n/a	n/a
21	GATA3	chr16:80871370-80872257	T-47D	breast:	n/a	chr16:80871631-80871640 chr16:80871631-80871638
22	JUND	chr16:80870730-80872067	Hela-S3	cervix:	n/a	n/a
23	SIN3AK20	chr16:80871387-80872260	MCF-7	breast:	n/a	n/a
24	FOXA1	chr16:80871434-80872400	T-47D	breast:	n/a	chr16:80871831-80871843
25	FOXA1	chr16:80871520-80872128	T-47D	breast:	n/a	chr16:80871831-80871843
26	BRCA1	chr16:80870805-80872128	Hela-S3	cervix:	n/a	n/a
27	NFYB	chr16:80871109-80872089	Hela-S3	cervix:	n/a	n/a
28	NFYA	chr16:80871101-80872214	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr16:80870107-80872211	Hela-S3	cervix:	n/a	chr16:80871547-80871559
30	MAZ	chr16:80871408-80872226	Hela-S3	cervix:	n/a	n/a
31	TCF12	chr16:80871172-80872220	MCF-7	breast:	n/a	chr16:80872106-80872113
32	FOXM1	chr16:80871391-80872100	MCF-7	breast:	n/a	n/a
33	ZNF143	chr16:80871749-80872169	Hela-S3	cervix:	n/a	n/a
34	GATA3	chr16:80871338-80872266	MCF-7	breast:	n/a	chr16:80871631-80871640 chr16:80871631-80871638
35	GATA3	chr16:80871274-80872217	MCF-7	breast:	n/a	chr16:80871631-80871640 chr16:80871631-80871638
36	ESR1	chr16:80871304-80872110	T-47D	breast:	n/a	n/a
37	ELK4	chr16:80871594-80872092	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr16:80870755-80872249	Hela-S3	cervix:	n/a	n/a
39	TFAP2A	chr16:80871570-80872195	Hela-S3	cervix:	n/a	chr16:80871751-80871761 chr16:80871751-80871761
40	GATA3	chr16:80871378-80872133	T-47D	breast:	n/a	chr16:80871631-80871640 chr16:80871631-80871638
41	POLR2A	chr16:80870644-80872386	Hela-S3	cervix:	n/a	n/a
42	TBP	chr16:80870103-80872176	Hela-S3	cervix:	n/a	n/a
43	MAX	chr16:80869976-80872277	Hela-S3	cervix:	n/a	n/a
44	MAFK	chr16:80870870-80872111	Hela-S3	cervix:	n/a	chr16:80871504-80871515

No.	Distal block	Cell Line	Cell type
1	chr11:68039642..68040173-chr16:80871534..80872505,2	Hela-S3	cervix:
2	chr16:80868740..80871247-chr16:80871583..80874485,2	K562	blood:
3	chr11:62608717..62609643-chr16:80871985..80872594,2	Hela-S3	cervix:
4	chr16:80871528..80872444-chr6:26056113..26056674,2	Hela-S3	cervix:
5	chr16:80837354..80839278-chr16:80870353..80872624,2	MCF-7	breast:
6	chr16:80871769..80873750-chr16:80874253..80880018,5	MCF-7	breast:
7	chr16:80650294..80652166-chr16:80871935..80873691,2	MCF-7	breast:
8	chr16:80868740..80871247-chr16:80871583..80874562,3	K562	blood:
9	chr16:80655167..80656068-chr16:80871542..80872135,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDYL2-4	chr16:80871829-80872402	XLOC_012021

Variant related genes	Relation type
ENSG00000260896	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000166446	Chromatin interaction
ENSG00000260896	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16954130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2549911	0.85[AMR][1000 genomes]
rs28448699	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55696405	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59241015	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61153381	0.83[AMR][1000 genomes]
rs61281082	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7193908	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7197605	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7197817	1.00[EUR][1000 genomes]
rs74028804	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028805	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028808	1.00[EUR][1000 genomes]
rs74028811	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028812	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028813	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028815	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028817	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028818	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74028821	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74030451	0.83[AMR][1000 genomes]
rs74030452	0.83[AMR][1000 genomes]
rs74030453	0.83[AMR][1000 genomes]
rs74030476	1.00[EUR][1000 genomes]
rs74030484	1.00[EUR][1000 genomes]
rs74030485	1.00[EUR][1000 genomes]
rs8051051	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8058054	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3451298	chr16:80696935-80997389	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3350075	chr16:80696955-80997359	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv542990	chr16:80729797-80918198	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv833301	chr16:80732170-80928751	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	esv2761922	chr16:80871113-80892858	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80870200-80872800	Enhancers	Placenta	Placenta
2	chr16:80870800-80872200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr16:80871400-80873600	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links