Variant report

Variant	rs55780735
Chromosome Location	chr16:69740374-69740375
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	POLR2A	chr16:69740351-69740600	GM12878	blood:	n/a	n/a
2	CEBPB	chr16:69740172-69740539	ECC-1	luminal epithelium:	n/a	chr16:69740306-69740317
3	FOS	chr16:69740149-69740459	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr16:69740154-69740512	MCF-7	breast:	n/a	chr16:69740306-69740317
5	POLR2A	chr16:69740299-69740575	U87	brain:	n/a	n/a
6	JUND	chr16:69740192-69740475	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:69739961-69741242	K562	blood:	n/a	n/a
8	STAT3	chr16:69740253-69740460	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr16:69740186-69740451	K562	blood:	n/a	n/a
10	CEBPB	chr16:69739947-69740750	HCT-116	colon:	n/a	chr16:69740306-69740317
11	CEBPB	chr16:69740212-69740421	HepG2	liver:	n/a	chr16:69740306-69740317
12	POLR2A	chr16:69739930-69743902	HepG2	liver:	n/a	n/a
13	POLR2A	chr16:69740230-69741152	U87	brain:	n/a	n/a
14	CEBPB	chr16:69740126-69740479	IMR90	lung:	n/a	chr16:69740306-69740317
15	POLR2A	chr16:69739832-69743980	A549	lung:	n/a	n/a
16	POLR2A	chr16:69740334-69740875	PANC-1	pancreas:	n/a	n/a
17	CEBPB	chr16:69740119-69740511	Hela-S3	cervix:	n/a	chr16:69740306-69740317
18	MAFK	chr16:69740106-69740436	HepG2	liver:	n/a	n/a
19	CEBPB	chr16:69740207-69740468	H1-hESC	embryonic stem cell:	n/a	chr16:69740306-69740317
20	CEBPB	chr16:69740069-69740550	MCF-7	breast:	n/a	chr16:69740306-69740317
21	CEBPB	chr16:69740079-69740551	A549	lung:	n/a	chr16:69740306-69740317
22	POLR2A	chr16:69740281-69740992	GM12891	blood:	n/a	n/a
23	POLR2A	chr16:69740169-69742240	HCT-116	colon:	n/a	n/a
24	CEBPB	chr16:69740137-69740493	A549	lung:	n/a	chr16:69740306-69740317
25	BCL3	chr16:69740012-69743000	A549	lung:	n/a	n/a
26	CEBPB	chr16:69740143-69740499	K562	blood:	n/a	chr16:69740306-69740317
27	CEBPB	chr16:69740069-69740636	A549	lung:	n/a	chr16:69740306-69740317
28	CEBPB	chr16:69740136-69740471	K562	blood:	n/a	chr16:69740306-69740317
29	STAT3	chr16:69740147-69740462	MCF10A-Er-Src	breast:	n/a	n/a
30	EP300	chr16:69740197-69740490	Hela-S3	cervix:	n/a	n/a
31	CEBPB	chr16:69740235-69740428	K562	blood:	n/a	chr16:69740306-69740317
32	FOS	chr16:69740164-69740405	MCF10A-Er-Src	breast:	n/a	n/a
33	CEBPB	chr16:69740075-69740501	HCT-116	colon:	n/a	chr16:69740306-69740317
34	POLR2A	chr16:69740136-69741099	HepG2	liver:	n/a	n/a
35	CEBPB	chr16:69740123-69740475	ECC-1	luminal epithelium:	n/a	chr16:69740306-69740317
36	CEBPB	chr16:69740134-69740501	HepG2	liver:	n/a	chr16:69740306-69740317
37	CEBPB	chr16:69740165-69740475	HepG2	liver:	n/a	chr16:69740306-69740317
38	MAFK	chr16:69740104-69740397	Hela-S3	cervix:	n/a	n/a
39	STAT3	chr16:69740267-69740467	MCF10A-Er-Src	breast:	n/a	n/a
40	CEBPB	chr16:69740176-69740487	HepG2	liver:	n/a	chr16:69740306-69740317
41	POLR2A	chr16:69740203-69740806	HepG2	liver:	n/a	n/a
42	FOS	chr16:69740158-69740419	MCF10A-Er-Src	breast:	n/a	n/a
43	MAFK	chr16:69740117-69740403	HepG2	liver:	n/a	n/a
44	JUN	chr16:69740198-69740447	HepG2	liver:	n/a	chr16:69740303-69740316

No.	Distal block	Cell Line	Cell type
1	chr16:69739781..69742163-chr16:69797369..69799073,2	MCF-7	breast:
2	chr16:69734561..69737941-chr16:69738671..69742586,5	MCF-7	breast:
3	chr16:69740285..69743443-chr16:69794568..69797700,3	MCF-7	breast:
4	chr16:69739403..69742355-chr16:69743812..69745961,3	MCF-7	breast:
5	chr16:69738931..69740863-chr16:69751048..69753277,2	K562	blood:

Variant related genes	Relation type
ENSG00000261602	TF binding region
ENSG00000260772	Chromatin interaction
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11075729	0.80[AMR][1000 genomes]
rs11640319	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12918548	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12921782	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12924052	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12933210	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469908	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1837016	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2017448	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2161630	0.80[AMR][1000 genomes]
rs2917670	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917671	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917677	0.82[AFR][1000 genomes]
rs2917678	0.82[ASN][1000 genomes]
rs2965749	0.82[ASN][1000 genomes]
rs3811348	0.81[EUR][1000 genomes]
rs3848278	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs45488899	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4633710	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6499241	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6499244	0.81[AFR][1000 genomes]
rs7187634	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7189878	0.84[AMR][1000 genomes]
rs7191292	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7192380	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7192543	0.80[AMR][1000 genomes]
rs8045432	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8049728	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8055756	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8061052	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9938213	0.86[AMR][1000 genomes];0.85[ASN][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	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
3	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:69726000-69755800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
4	chr16:69726800-69747600	Weak transcription	Fetal Heart	heart
5	chr16:69728200-69746200	Weak transcription	Stomach Mucosa	stomach
6	chr16:69728200-69758600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr16:69728400-69744200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:69728400-69748800	Weak transcription	Gastric	stomach
9	chr16:69728400-69759200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:69728600-69752000	Weak transcription	Fetal Brain Male	brain
11	chr16:69729200-69745000	Weak transcription	Spleen	Spleen
12	chr16:69729400-69741400	Weak transcription	Lung	lung
13	chr16:69729400-69741600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr16:69729400-69743600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr16:69729400-69744800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr16:69729400-69745000	Weak transcription	Pancreas	Pancrea
17	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
18	chr16:69729400-69760000	Weak transcription	Ovary	ovary
19	chr16:69729600-69740800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr16:69729600-69745000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:69729800-69746200	Weak transcription	Aorta	Aorta
22	chr16:69729800-69746200	Weak transcription	Left Ventricle	heart
23	chr16:69729800-69748800	Weak transcription	Esophagus	oesophagus
24	chr16:69730000-69740600	Weak transcription	Small Intestine	intestine
25	chr16:69730000-69743400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr16:69730000-69743400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr16:69730000-69743600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:69730000-69745200	Weak transcription	Thymus	Thymus
29	chr16:69730000-69745800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr16:69730000-69759000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr16:69730200-69742600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr16:69730200-69743400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr16:69730200-69743400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr16:69730200-69746000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr16:69730400-69741800	Weak transcription	Brain Hippocampus Middle	brain
36	chr16:69730400-69744800	Weak transcription	Colonic Mucosa	Colon
37	chr16:69730400-69747000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr16:69730600-69743600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr16:69730600-69759800	Weak transcription	Fetal Brain Female	brain
40	chr16:69730800-69744600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr16:69730800-69759800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr16:69731000-69746000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr16:69731600-69743600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr16:69731800-69741400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr16:69731800-69744400	Weak transcription	K562	blood
46	chr16:69731800-69745000	Weak transcription	Hela-S3	cervix
47	chr16:69731800-69746200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr16:69731800-69759600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr16:69731800-69759800	Weak transcription	Primary B cells from cord blood	blood
50	chr16:69731800-69759800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links