Variant report

Variant	rs16945824
Chromosome Location	chr16:48151489-48151490
allele	C/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	MTA3	chr16:48151449-48151748	GM12878	blood:	n/a	n/a
2	CTCF	chr16:48151480-48151630	GM12864	blood:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562
3	SMC3	chr16:48151415-48151720	Hela-S3	cervix:	n/a	chr16:48151685-48151699 chr16:48151548-48151558 chr16:48151548-48151562
4	RAD21	chr16:48151379-48151828	HepG2	liver:	n/a	chr16:48151689-48151699 chr16:48151544-48151563 chr16:48151547-48151560 chr16:48151550-48151564 chr16:48151687-48151700
5	CTCF	chr16:48151480-48151630	HCT-116	colon:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562
6	ELF1	chr16:48151362-48151694	K562	blood:	n/a	n/a
7	PAX5	chr16:48151406-48151753	GM12878	blood:	n/a	n/a
8	JUND	chr16:48151417-48151716	K562	blood:	n/a	n/a
9	EGR1	chr16:48151437-48151975	K562	blood:	n/a	chr16:48151844-48151859 chr16:48151845-48151858 chr16:48151647-48151661 chr16:48151583-48151607 chr16:48151845-48151858 chr16:48151845-48151858
10	CTCF	chr16:48151425-48151775	H1-hESC	embryonic stem cell:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
11	RUNX3	chr16:48151393-48151751	GM12878	blood:	n/a	n/a
12	CTCF	chr16:48151404-48151884	GM19240	blood:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
13	CTCF	chr16:48151460-48151610	WI-38	lung:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562
14	CTCF	chr16:48151353-48151870	HCT-116	colon:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
15	CTCFL	chr16:48151401-48151650	K562	blood:	n/a	chr16:48151548-48151557
16	CTCF	chr16:48151119-48152473	A549	lung:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
17	CEBPB	chr16:48151359-48151726	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr16:48151425-48151745	Medullo	brain:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
19	ATF2	chr16:48151421-48151744	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr16:48151178-48151947	A549	lung:	n/a	chr16:48151689-48151699 chr16:48151544-48151563 chr16:48151547-48151560 chr16:48151550-48151564 chr16:48151687-48151700 chr16:48151295-48151308
21	CTCF	chr16:48151475-48151694	GM13976	blood:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562
22	ELF1	chr16:48151402-48151692	HepG2	liver:	n/a	n/a
23	CTCF	chr16:48151460-48151610	HCT-116	colon:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562
24	YY1	chr16:48151325-48151686	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZMIZ1	chr16:48151481-48151783	K562	blood:	n/a	n/a
26	CTCF	chr16:48151425-48151753	A549	lung:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
27	MYC	chr16:48151461-48151492	HepG2	liver:	n/a	n/a
28	RAD21	chr16:48151000-48152004	SK-N-SH	brain:	n/a	chr16:48151689-48151699 chr16:48151544-48151563 chr16:48151547-48151560 chr16:48151550-48151564 chr16:48151687-48151700 chr16:48151295-48151308
29	CTCF	chr16:48151439-48151708	SK-N-SH_RA	brain:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
30	CTCF	chr16:48151440-48151728	HUVEC	blood vessel:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
31	YY1	chr16:48151453-48151718	GM12878	blood:	n/a	n/a
32	MAZ	chr16:48151169-48151904	IMR90	lung:	n/a	n/a
33	CTCF	chr16:48151429-48151712	SK-N-SH_RA	brain:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
34	ZNF143	chr16:48151377-48151757	GM12878	blood:	n/a	n/a
35	CTCF	chr16:48151480-48151630	GM06990	blood:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562
36	CTCF	chr16:48151389-48151708	T-47D	breast:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
37	RAD21	chr16:48151370-48151719	K562	blood:	n/a	chr16:48151689-48151699 chr16:48151544-48151563 chr16:48151547-48151560 chr16:48151550-48151564 chr16:48151687-48151700
38	TCF12	chr16:48151427-48151656	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr16:48151371-48151925	K562	blood:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
40	CTCF	chr16:48151285-48151945	K562	blood:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699
41	MYC	chr16:48151443-48151710	NB4	blood:	n/a	n/a
42	SMC3	chr16:48151359-48151793	GM12878	blood:	n/a	chr16:48151685-48151699 chr16:48151548-48151558 chr16:48151548-48151562
43	ZBTB7A	chr16:48151460-48151834	HepG2	liver:	n/a	n/a
44	RAD21	chr16:48151387-48151704	GM12878	blood:	n/a	chr16:48151689-48151699 chr16:48151544-48151563 chr16:48151547-48151560 chr16:48151550-48151564 chr16:48151687-48151700
45	CTCF	chr16:48151460-48151610	RPTEC	kidney:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562
46	ZBTB7A	chr16:48151438-48151720	K562	blood:	n/a	n/a
47	HCFC1	chr16:48151408-48151723	K562	blood:	n/a	n/a
48	RAD21	chr16:48151360-48151811	HepG2	liver:	n/a	chr16:48151689-48151699 chr16:48151544-48151563 chr16:48151547-48151560 chr16:48151550-48151564 chr16:48151687-48151700
49	RAD21	chr16:48151362-48151815	IMR90	lung:	n/a	chr16:48151689-48151699 chr16:48151544-48151563 chr16:48151547-48151560 chr16:48151550-48151564 chr16:48151687-48151700
50	CTCF	chr16:48151424-48151754	MCF-7	breast:	n/a	chr16:48151548-48151561 chr16:48151547-48151563 chr16:48151553-48151561 chr16:48151548-48151561 chr16:48151546-48151564 chr16:48151541-48151562 chr16:48151686-48151699

No.	Distal block	Cell Line	Cell type
1	chr16:47071556..47072334-chr16:48151095..48151940,2	K562	blood:
2	chr16:48151208..48152156-chr16:48190003..48191037,5	MCF-7	breast:
3	chr16:48151213..48152149-chr16:48190361..48191030,3	K562	blood:
4	chr16:46981810..46982328-chr16:48151170..48152007,2	K562	blood:
5	chr16:48151282..48152129-chr16:48198404..48199139,3	MCF-7	breast:
6	chr11:66383462..66384208-chr16:48151167..48151823,2	HCT-116	colon:
7	chr16:47238697..47239501-chr16:48151319..48151975,2	MCF-7	breast:
8	chr16:48151128..48152237-chr16:48190393..48191453,6	MCF-7	breast:

Variant related genes	Relation type
ABCC12	TF binding region
ENSG00000239306	Chromatin interaction
ENSG00000248643	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11861448	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs11864016	1.00[EUR][1000 genomes]
rs11864570	1.00[EUR][1000 genomes]
rs12103132	1.00[EUR][1000 genomes]
rs13330281	1.00[EUR][1000 genomes]
rs13330882	1.00[EUR][1000 genomes]
rs13331266	0.89[ASW][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13333718	1.00[EUR][1000 genomes]
rs13334423	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs13334475	1.00[EUR][1000 genomes]
rs13335010	1.00[EUR][1000 genomes]
rs1345425	1.00[EUR][1000 genomes]
rs16945786	1.00[EUR][1000 genomes]
rs16945813	1.00[EUR][1000 genomes]
rs16945816	1.00[EUR][1000 genomes]
rs16945819	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945828	1.00[EUR][1000 genomes]
rs16945831	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945835	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16945839	0.89[ASW][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945860	1.00[EUR][1000 genomes]
rs2016940	1.00[EUR][1000 genomes]
rs28431782	1.00[EUR][1000 genomes]
rs28526661	1.00[EUR][1000 genomes]
rs28531369	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587611	1.00[EUR][1000 genomes]
rs28592871	1.00[EUR][1000 genomes]
rs28669266	1.00[EUR][1000 genomes]
rs34106426	1.00[EUR][1000 genomes]
rs4785405	1.00[EUR][1000 genomes]
rs4785406	1.00[MEX][hapmap]
rs56093600	1.00[EUR][1000 genomes]
rs57124014	1.00[EUR][1000 genomes]
rs57432729	1.00[EUR][1000 genomes]
rs57740199	1.00[EUR][1000 genomes]
rs58204235	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58622309	1.00[EUR][1000 genomes]
rs59311846	1.00[EUR][1000 genomes]
rs59312258	1.00[EUR][1000 genomes]
rs59466391	1.00[EUR][1000 genomes]
rs59528776	1.00[EUR][1000 genomes]
rs59766379	1.00[EUR][1000 genomes]
rs59832329	1.00[EUR][1000 genomes]
rs59966196	1.00[EUR][1000 genomes]
rs6500304	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6500305	1.00[EUR][1000 genomes]
rs7187069	1.00[EUR][1000 genomes]
rs7197701	1.00[EUR][1000 genomes]
rs7203314	1.00[EUR][1000 genomes]
rs73540833	1.00[EUR][1000 genomes]
rs73540845	1.00[EUR][1000 genomes]
rs73540853	1.00[EUR][1000 genomes]
rs74018249	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74018255	1.00[EUR][1000 genomes]
rs8046592	1.00[EUR][1000 genomes]
rs8048367	1.00[EUR][1000 genomes]
rs8056553	1.00[EUR][1000 genomes]
rs8058288	1.00[EUR][1000 genomes]
rs9302750	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs939360	1.00[EUR][1000 genomes]
rs939362	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs961668	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs9925287	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs9926338	1.00[EUR][1000 genomes]
rs9933094	1.00[EUR][1000 genomes]
rs9933277	1.00[EUR][1000 genomes]
rs9935027	1.00[EUR][1000 genomes]
rs9936500	1.00[EUR][1000 genomes]
rs9936532	1.00[EUR][1000 genomes]
rs9938810	1.00[EUR][1000 genomes]
rs9940987	1.00[MEX][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520355	chr16:47424828-48164777	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1059259	chr16:48113396-48304404	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv542916	chr16:48113396-48304404	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48146400-48160600	Weak transcription	Right Atrium	heart
2	chr16:48147600-48160600	Weak transcription	Psoas Muscle	Psoas
3	chr16:48151000-48152200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:48151000-48152800	Enhancers	A549	lung
5	chr16:48151000-48153200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr16:48151200-48151600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
7	chr16:48151200-48151600	Enhancers	Right Ventricle	heart
8	chr16:48151200-48151600	Enhancers	Spleen	Spleen
9	chr16:48151200-48151600	Flanking Active TSS	HepG2	liver
10	chr16:48151200-48151800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr16:48151200-48151800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr16:48151200-48151800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr16:48151200-48152000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr16:48151200-48152000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:48151400-48151600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:48151400-48151600	Bivalent Enhancer	Placenta	Placenta
17	chr16:48151400-48151800	Enhancers	Lung	lung
18	chr16:48151400-48152000	Enhancers	Pancreas	Pancrea
19	chr16:48151400-48152200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr16:48151400-48152200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr16:48151400-48152400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr16:48151400-48152400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr16:48151400-48157000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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