Variant report

Variant	rs3743591
Chromosome Location	chr16:12059032-12059033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:110 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:12058994-12059132	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr16:12057501-12061734	GM18505	blood:	n/a	n/a
3	YY1	chr16:12058479-12059159	GM12878	blood:	n/a	n/a
4	EBF1	chr16:12058524-12059147	GM12878	blood:	n/a	n/a
5	BCLAF1	chr16:12058547-12059574	GM12878	blood:	n/a	n/a
6	ATF2	chr16:12058461-12059383	GM12878	blood:	n/a	n/a
7	SIN3A	chr16:12058705-12059438	GM12878	blood:	n/a	n/a
8	CEBPB	chr16:12058795-12059231	GM12878	blood:	n/a	chr16:12058947-12058964
9	POLR2A	chr16:12058126-12059489	GM12892	blood:	n/a	n/a
10	TCF3	chr16:12058500-12059134	GM12878	blood:	n/a	n/a
11	IRF4	chr16:12058550-12059285	GM12878	blood:	n/a	chr16:12058905-12058919
12	RELA	chr16:12058647-12059451	GM18505	blood:	n/a	n/a
13	RELA	chr16:12058644-12059295	GM19099	blood:	n/a	n/a
14	NFATC1	chr16:12058602-12059373	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:12058079-12060586	GM19099	blood:	n/a	n/a
16	RCOR1	chr16:12058621-12059274	GM12878	blood:	n/a	n/a
17	POLR2A	chr16:12057110-12063123	GM12891	blood:	n/a	n/a
18	POLR2A	chr16:12058594-12059189	GM12878	blood:	n/a	n/a
19	TCF3	chr16:12058577-12059198	GM12878	blood:	n/a	n/a
20	FOXM1	chr16:12057921-12059317	GM12878	blood:	n/a	n/a
21	YY1	chr16:12058524-12059047	GM12891	blood:	n/a	n/a
22	CUX1	chr16:12058680-12059153	GM12878	blood:	n/a	n/a
23	POLR2A	chr16:12059015-12059563	MCF10A-Er-Src	breast:	n/a	n/a
24	NFIC	chr16:12057945-12059686	GM12878	blood:	n/a	n/a
25	MXI1	chr16:12058557-12059467	IMR90	lung:	n/a	n/a
26	EP300	chr16:12058211-12059327	GM12878	blood:	n/a	n/a
27	BCL3	chr16:12058576-12059193	GM12878	blood:	n/a	n/a
28	MTA3	chr16:12057615-12059791	GM12878	blood:	n/a	n/a
29	MTA3	chr16:12058533-12059504	GM12878	blood:	n/a	n/a
30	POLR2A	chr16:12058472-12059376	GM12892	blood:	n/a	n/a
31	POLR2A	chr16:12058601-12059670	GM12878	blood:	n/a	n/a
32	PAX5	chr16:12058769-12059092	GM12878	blood:	n/a	n/a
33	STAT3	chr16:12058545-12059309	GM12878	blood:	n/a	chr16:12058906-12058917
34	BATF	chr16:12058751-12059152	GM12878	blood:	n/a	n/a
35	MEF2A	chr16:12058530-12059234	GM12878	blood:	n/a	chr16:12058891-12058906 chr16:12058894-12058903 chr16:12058893-12058904 chr16:12058891-12058907
36	STAT1	chr16:12058748-12059259	GM12878	blood:	n/a	chr16:12058906-12058917
37	PAX5	chr16:12058528-12059336	GM12878	blood:	n/a	n/a
38	RUNX3	chr16:12058508-12059325	GM12878	blood:	n/a	n/a
39	RELA	chr16:12058542-12059356	GM10847	blood:	n/a	n/a
40	EP300	chr16:12058702-12059454	GM12878	blood:	n/a	chr16:12059418-12059432
41	POLR2A	chr16:12058084-12060502	GM15510	blood:	n/a	n/a
42	POLR2A	chr16:12058143-12059264	GM12878	blood:	n/a	n/a
43	BCL11A	chr16:12058632-12059097	GM12878	blood:	n/a	n/a
44	TAF1	chr16:12058539-12059335	GM12878	blood:	n/a	n/a
45	FOXM1	chr16:12058395-12059398	GM12878	blood:	n/a	n/a
46	IKZF1	chr16:12058025-12059355	GM12878	blood:	n/a	n/a
47	POLR2A	chr16:12058025-12059338	GM18951	blood:	n/a	n/a
48	RELA	chr16:12058579-12059195	GM19193	blood:	n/a	n/a
49	POLR2A	chr16:12058546-12059433	GM12891	blood:	n/a	n/a
50	ZMIZ1	chr16:12059032-12059073	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:12059019-12059069	SAEC	small airway:	n/a
2	chr16:12059019-12059069	SKMC	muscle:	n/a
3	chr16:12059019-12059069	LNCaP	prostate:	n/a
4	chr16:12059019-12059069	GM06990	blood:	n/a
5	chr16:12059019-12059069	HCPEpiC	choroid plexus:	n/a
6	chr16:12059019-12059069	U87	brain:	n/a
7	chr16:12059019-12059069	NB4	blood:	n/a
8	chr16:12059019-12059069	PrEC	prostate:	n/a
9	chr16:12059019-12059069	A549	lung:	n/a
10	chr16:12059019-12059069	HNPCEpiC	eye:	n/a
11	chr16:12059019-12059069	Caco-2	colon:	n/a
12	chr16:12059019-12059069	GM19239	blood:	n/a
13	chr16:12059019-12059069	HPAEpiC	pulmonary alveolar:	n/a
14	chr16:12059019-12059069	Hela-S3	cervix:	n/a
15	chr16:12059019-12059069	HCF	heart:	n/a
16	chr16:12059019-12059069	HUVEC	blood vessel:	n/a
17	chr16:12059019-12059069	BJ	skin:	n/a
18	chr16:12059019-12059069	AoSMC	blood vessel:	n/a
19	chr16:12059019-12059069	ECC-1	luminal epithelium:	n/a
20	chr16:12059019-12059069	HRPEpiC	eye:	n/a
21	chr16:12059019-12059069	HAEpiC	amniotic membrane:	n/a
22	chr16:12059019-12059069	AG04449	skin:	fetal
23	chr16:12059019-12059069	HEEpiC	esophagus:	n/a
24	chr16:12059019-12059069	PANC-1	pancreas:	n/a
25	chr16:12059019-12059069	CMK	blood:	n/a
26	chr16:12059019-12059069	ovcar-3	ovarian:	n/a
27	chr16:12059019-12059069	GM12878	blood:	n/a
28	chr16:12059019-12059069	NT2-D1	testis:	n/a
29	chr16:12059019-12059069	MCF10A-Er-Src	breast:	n/a
30	chr16:12059019-12059069	Jurkat	blood:	n/a
31	chr16:12059019-12059069	PFSK-1	brain:	n/a
32	chr16:12059019-12059069	GM12892	blood:	n/a
33	chr16:12059019-12059069	AG04450	lung:	fetal
34	chr16:12059019-12059069	H1-hESC	embryonic stem cell:	embryo
35	chr16:12059019-12059069	IMR90	lung:	fetal
36	chr16:12059019-12059069	HepG2	liver:	n/a
37	chr16:12059019-12059069	Hepatocyte	liver:	n/a
38	chr16:12059019-12059069	HMEC	breast:	n/a
39	chr16:12059019-12059069	SK-N-SH_RA	brain:	n/a
40	chr16:12059019-12059069	HL-60	blood:	n/a
41	chr16:12059019-12059069	BE2_C	brain:	n/a
42	chr16:12059019-12059069	AG09319	gingival:	n/a
43	chr16:12059019-12059069	AG09309	skin:	n/a
44	chr16:12059019-12059069	SK-N-SH	brain:	n/a
45	chr16:12059019-12059069	HEK293	kidney:	embryo
46	chr16:12059019-12059069	AG10803	skin:	n/a
47	chr16:12059019-12059069	SK-N-MC	brain:	n/a
48	chr16:12059019-12059069	NHDF-neo	bronchial:	n/a
49	chr16:12059019-12059069	ProgFib	skin:	n/a
50	chr16:12059019-12059069	HIPEpiC	eye:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12058363..12061770-chr16:12069205..12072370,4	MCF-7	breast:

No data

Variant related genes	Relation type
TNFRSF17	TF binding region
TNFRSF17	CpG island
ENSG00000048471	Chromatin interaction
ENSG00000260488	Chromatin interaction
ENSG00000234719	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10451099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10468251	0.91[ASN][1000 genomes]
rs10852345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10852346	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11075035	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11075036	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075037	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11570137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11570173	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11864397	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12597378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12926535	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12927256	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12928141	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12929036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12929544	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12929852	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12933691	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12934607	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2017662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35965279	0.84[ASN][1000 genomes]
rs365423	0.89[ASN][1000 genomes]
rs366262	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851002	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851003	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs387871	0.90[ASN][1000 genomes]
rs3916675	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57171695	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58398910	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59320000	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6498255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6498256	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6498257	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7189024	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7190636	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7191310	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7195514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72782778	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8046211	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8047277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8051343	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8055129	0.94[ASN][1000 genomes]
rs8060611	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8062121	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9922422	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9922795	0.81[EUR][1000 genomes];0.90[ASN][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	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv571459	chr16:12046899-12062396	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv962195	chr16:12053526-12071576	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12040400-12065400	Weak transcription	Fetal Intestine Small	intestine
2	chr16:12042200-12064400	Weak transcription	Fetal Stomach	stomach
3	chr16:12048600-12064800	Weak transcription	Thymus	Thymus
4	chr16:12052200-12067600	Weak transcription	Osteobl	bone
5	chr16:12052200-12069600	Weak transcription	Primary T cells from cord blood	blood
6	chr16:12052400-12066800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:12053000-12065800	Weak transcription	Placenta	Placenta
8	chr16:12054600-12069400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr16:12056800-12069400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr16:12057000-12060000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:12057400-12059400	Enhancers	K562	blood
14	chr16:12057600-12059800	Enhancers	Fetal Thymus	thymus
15	chr16:12058200-12059400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr16:12058200-12059400	Bivalent Enhancer	HepG2	liver
17	chr16:12058200-12061200	Active TSS	GM12878-XiMat	blood
18	chr16:12058600-12059200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:12058600-12059200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr16:12058600-12059200	Enhancers	Brain Angular Gyrus	brain
21	chr16:12058600-12059200	Enhancers	Brain Hippocampus Middle	brain
22	chr16:12058600-12059400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr16:12058600-12059400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr16:12058600-12059400	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr16:12058600-12059400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr16:12058600-12059400	Enhancers	Brain Anterior Caudate	brain
27	chr16:12058600-12059400	Enhancers	Brain Substantia Nigra	brain
28	chr16:12058600-12059800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr16:12058800-12059400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:12058800-12059400	Enhancers	NHEK	skin
31	chr16:12058800-12059600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr16:12058800-12059600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr16:12058800-12067600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr16:12058800-12069400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr16:12059000-12059200	Enhancers	Adipose Nuclei	Adipose
36	chr16:12059000-12059400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr16:12059000-12059400	Enhancers	Brain Cingulate Gyrus	brain
38	chr16:12059000-12059400	Enhancers	NHDF-Ad	bronchial
39	chr16:12059000-12061200	Active TSS	Duodenum Mucosa	Duodenum
40	chr16:12059000-12061800	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr16:12059000-12069400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr16:12059000-12069400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr16:12059000-12069400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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