Variant report

Variant	rs13334681
Chromosome Location	chr16:72118065-72118066
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	POLR2A	chr16:72116485-72119281	K562	blood:	n/a	n/a
2	HNF4A	chr16:72117624-72118241	HepG2	liver:	n/a	chr16:72117855-72117870
3	FOXA2	chr16:72117699-72118191	HepG2	liver:	n/a	n/a
4	EP300	chr16:72117705-72118239	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:72117782-72118081	K562	blood:	n/a	n/a
6	HNF4A	chr16:72117703-72118133	HepG2	liver:	n/a	chr16:72117855-72117870
7	CEBPB	chr16:72117915-72118203	K562	blood:	n/a	chr16:72118069-72118080
8	FOXA1	chr16:72117681-72118122	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:72117734-72118157	HepG2	liver:	n/a	n/a
10	HNF4A	chr16:72117610-72118184	HepG2	liver:	n/a	chr16:72117855-72117870
11	MYBL2	chr16:72117609-72118196	HepG2	liver:	n/a	n/a
12	NFIC	chr16:72117679-72118176	HepG2	liver:	n/a	n/a
13	HNF4G	chr16:72117701-72118218	HepG2	liver:	n/a	n/a
14	JUN	chr16:72117911-72118215	HepG2	liver:	n/a	chr16:72118070-72118083
15	FOXA1	chr16:72117696-72118104	HepG2	liver:	n/a	n/a
16	CEBPB	chr16:72117925-72118194	H1-hESC	embryonic stem cell:	n/a	chr16:72118069-72118080
17	CEBPB	chr16:72117940-72118170	HepG2	liver:	n/a	chr16:72118069-72118080
18	CEBPB	chr16:72117912-72118199	IMR90	lung:	n/a	chr16:72118069-72118080
19	HDAC2	chr16:72117708-72118199	HepG2	liver:	n/a	n/a
20	CEBPB	chr16:72117649-72118254	HepG2	liver:	n/a	chr16:72118069-72118080
21	BRCA1	chr16:72118060-72118078	GM12878	blood:	n/a	n/a
22	POLR2A	chr16:72117590-72118178	GM12878	blood:	n/a	n/a
23	HNF4G	chr16:72117530-72118112	HepG2	liver:	n/a	n/a
24	ARID3A	chr16:72117697-72118127	HepG2	liver:	n/a	n/a
25	CEBPB	chr16:72117900-72118147	A549	lung:	n/a	chr16:72118069-72118080
26	CEBPB	chr16:72117677-72118233	HepG2	liver:	n/a	chr16:72118069-72118080
27	JUND	chr16:72117672-72118200	HepG2	liver:	n/a	n/a
28	POLR2A	chr16:72117761-72118170	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72117553..72119364-chr16:72127046..72129363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260252	TF binding region
ENSG00000140829	Chromatin interaction
ENSG00000140830	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1049933	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12325171	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12325593	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs13332560	0.85[AMR][1000 genomes]
rs13333207	0.85[AMR][1000 genomes]
rs13335854	0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs13338949	1.00[AMR][1000 genomes]
rs16970697	1.00[AMR][1000 genomes]
rs16973640	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973723	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs28455724	0.85[AMR][1000 genomes]
rs28483075	0.85[AMR][1000 genomes]
rs28507713	1.00[AMR][1000 genomes]
rs28557204	1.00[AMR][1000 genomes]
rs28610193	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28639994	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35184823	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4788614	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs56978453	1.00[AMR][1000 genomes]
rs57024912	0.85[AMR][1000 genomes]
rs61074815	1.00[AMR][1000 genomes]
rs7184834	0.95[YRI][hapmap]
rs7186117	0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs7186448	1.00[AMR][1000 genomes]
rs7188150	0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs7188462	1.00[AMR][1000 genomes]
rs7189506	0.94[YRI][hapmap];0.85[AMR][1000 genomes]
rs7189654	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs7191270	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7191499	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7194569	1.00[AMR][1000 genomes]
rs7202157	0.83[AMR][1000 genomes]
rs7202158	0.83[AMR][1000 genomes]
rs7203195	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs73578560	1.00[AMR][1000 genomes]
rs73580679	1.00[AMR][1000 genomes]
rs73582412	1.00[AMR][1000 genomes]
rs8045316	0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs8047881	1.00[YRI][hapmap]
rs8051438	0.85[AMR][1000 genomes]
rs8052025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8055216	1.00[AMR][1000 genomes]
rs8056409	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8056752	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8057379	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs8061292	0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs8061439	0.85[AMR][1000 genomes]
rs9921052	0.85[AMR][1000 genomes]
rs9921752	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs9923961	1.00[AMR][1000 genomes]
rs9925476	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs9925493	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9928784	1.00[MEX][hapmap]
rs9932236	1.00[ASW][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs9932742	0.93[MKK][hapmap]
rs9933867	0.85[AMR][1000 genomes]
rs9934521	1.00[AMR][1000 genomes]
rs9940996	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs9972770	0.95[YRI][hapmap]

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	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
9	nsv9456	chr16:72084761-72118322	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
10	nsv978167	chr16:72088322-72118671	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
11	esv1808086	chr16:72088669-72128767	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a
12	esv3343168	chr16:72111500-72128436	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72090200-72118400	Weak transcription	Lung	lung
2	chr16:72093800-72118400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:72093800-72118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:72096800-72118200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr16:72102800-72118400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:72106400-72118200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:72106600-72126400	Weak transcription	Small Intestine	intestine
8	chr16:72107000-72118200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr16:72107000-72118200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr16:72108000-72126400	Weak transcription	Fetal Heart	heart
11	chr16:72108200-72118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr16:72108200-72118400	Weak transcription	Fetal Brain Female	brain
13	chr16:72108400-72118400	Weak transcription	Brain Anterior Caudate	brain
14	chr16:72108400-72118400	Weak transcription	Fetal Muscle Leg	muscle
15	chr16:72108400-72118400	Weak transcription	Right Ventricle	heart
16	chr16:72108400-72118600	Weak transcription	Colon Smooth Muscle	Colon
17	chr16:72108400-72119000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr16:72108600-72118400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr16:72108600-72118400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr16:72108600-72118400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr16:72108800-72118200	Weak transcription	Brain Substantia Nigra	brain
22	chr16:72108800-72118400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:72108800-72118600	Weak transcription	K562	blood
24	chr16:72108800-72118800	Weak transcription	Gastric	stomach
25	chr16:72109000-72118200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr16:72109000-72118400	Weak transcription	Right Atrium	heart
27	chr16:72109000-72118600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr16:72109000-72122600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr16:72109600-72118400	Weak transcription	Aorta	Aorta
30	chr16:72109600-72118400	Weak transcription	Pancreas	Pancrea
31	chr16:72109600-72118600	Weak transcription	Stomach Mucosa	stomach
32	chr16:72110000-72118200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr16:72110000-72118600	Weak transcription	HSMM	muscle
34	chr16:72110200-72122800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr16:72110600-72118400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr16:72110800-72118200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr16:72110800-72118400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr16:72111000-72120000	Weak transcription	NHLF	lung
39	chr16:72111200-72118200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr16:72111200-72118600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr16:72111400-72118400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr16:72112000-72118400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr16:72112000-72118400	Weak transcription	Spleen	Spleen
44	chr16:72112200-72118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr16:72112200-72118400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr16:72112600-72118200	Weak transcription	Ovary	ovary
47	chr16:72115400-72118200	Enhancers	HepG2	liver
48	chr16:72115600-72118400	Weak transcription	Fetal Intestine Large	intestine
49	chr16:72115800-72118400	Weak transcription	Fetal Brain Male	brain
50	chr16:72116000-72118600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links