Variant report

Variant	rs11570138
Chromosome Location	chr16:12058932-12058933
allele	C/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	chr16:12057501-12061734	GM18505	blood:	n/a	n/a
2	YY1	chr16:12058479-12059159	GM12878	blood:	n/a	n/a
3	EBF1	chr16:12058524-12059147	GM12878	blood:	n/a	n/a
4	BCLAF1	chr16:12058547-12059574	GM12878	blood:	n/a	n/a
5	ATF2	chr16:12058461-12059383	GM12878	blood:	n/a	n/a
6	SIN3A	chr16:12058705-12059438	GM12878	blood:	n/a	n/a
7	CEBPB	chr16:12058795-12059231	GM12878	blood:	n/a	chr16:12058947-12058964
8	POLR2A	chr16:12058126-12059489	GM12892	blood:	n/a	n/a
9	TCF3	chr16:12058500-12059134	GM12878	blood:	n/a	n/a
10	IRF4	chr16:12058550-12059285	GM12878	blood:	n/a	chr16:12058905-12058919
11	RELA	chr16:12058647-12059451	GM18505	blood:	n/a	n/a
12	RELA	chr16:12058644-12059295	GM19099	blood:	n/a	n/a
13	NFATC1	chr16:12058602-12059373	GM12878	blood:	n/a	n/a
14	POLR2A	chr16:12058079-12060586	GM19099	blood:	n/a	n/a
15	RCOR1	chr16:12058621-12059274	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:12057110-12063123	GM12891	blood:	n/a	n/a
17	POLR2A	chr16:12058594-12059189	GM12878	blood:	n/a	n/a
18	TCF3	chr16:12058577-12059198	GM12878	blood:	n/a	n/a
19	FOXM1	chr16:12057921-12059317	GM12878	blood:	n/a	n/a
20	YY1	chr16:12058524-12059047	GM12891	blood:	n/a	n/a
21	CUX1	chr16:12058680-12059153	GM12878	blood:	n/a	n/a
22	NFIC	chr16:12057945-12059686	GM12878	blood:	n/a	n/a
23	MXI1	chr16:12058557-12059467	IMR90	lung:	n/a	n/a
24	EP300	chr16:12058211-12059327	GM12878	blood:	n/a	n/a
25	BCL3	chr16:12058576-12059193	GM12878	blood:	n/a	n/a
26	MTA3	chr16:12057615-12059791	GM12878	blood:	n/a	n/a
27	MTA3	chr16:12058533-12059504	GM12878	blood:	n/a	n/a
28	POLR2A	chr16:12058472-12059376	GM12892	blood:	n/a	n/a
29	POLR2A	chr16:12058601-12059670	GM12878	blood:	n/a	n/a
30	PAX5	chr16:12058769-12059092	GM12878	blood:	n/a	n/a
31	STAT3	chr16:12058545-12059309	GM12878	blood:	n/a	chr16:12058906-12058917
32	BATF	chr16:12058751-12059152	GM12878	blood:	n/a	n/a
33	MEF2A	chr16:12058530-12059234	GM12878	blood:	n/a	chr16:12058891-12058906 chr16:12058894-12058903 chr16:12058893-12058904 chr16:12058891-12058907
34	STAT1	chr16:12058748-12059259	GM12878	blood:	n/a	chr16:12058906-12058917
35	PAX5	chr16:12058528-12059336	GM12878	blood:	n/a	n/a
36	RUNX3	chr16:12058508-12059325	GM12878	blood:	n/a	n/a
37	RELA	chr16:12058542-12059356	GM10847	blood:	n/a	n/a
38	EP300	chr16:12058702-12059454	GM12878	blood:	n/a	chr16:12059418-12059432
39	POLR2A	chr16:12058084-12060502	GM15510	blood:	n/a	n/a
40	POLR2A	chr16:12058143-12059264	GM12878	blood:	n/a	n/a
41	BCL11A	chr16:12058632-12059097	GM12878	blood:	n/a	n/a
42	TAF1	chr16:12058539-12059335	GM12878	blood:	n/a	n/a
43	FOXM1	chr16:12058395-12059398	GM12878	blood:	n/a	n/a
44	IKZF1	chr16:12058025-12059355	GM12878	blood:	n/a	n/a
45	POLR2A	chr16:12058025-12059338	GM18951	blood:	n/a	n/a
46	RELA	chr16:12058579-12059195	GM19193	blood:	n/a	n/a
47	POLR2A	chr16:12058546-12059433	GM12891	blood:	n/a	n/a
48	POU2F2	chr16:12058577-12059224	GM12891	blood:	n/a	chr16:12058998-12059006
49	PAX5	chr16:12058715-12059170	GM12891	blood:	n/a	n/a
50	BATF	chr16:12058550-12059280	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12008413..12010461-chr16:12056035..12059014,2	MCF-7	breast:
2	chr16:12058363..12061770-chr16:12069205..12072370,4	MCF-7	breast:

Variant related genes	Relation type
TNFRSF17	TF binding region
ENSG00000266163	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000260488	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000234719	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11570147	1.00[AFR][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:39 , 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	chr16:12055000-12059000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr16:12056800-12069400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr16:12057000-12060000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr16:12057000-12067600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:12057400-12059400	Enhancers	K562	blood
15	chr16:12057600-12059800	Enhancers	Fetal Thymus	thymus
16	chr16:12058200-12059000	Enhancers	Psoas Muscle	Psoas
17	chr16:12058200-12059400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr16:12058200-12059400	Bivalent Enhancer	HepG2	liver
19	chr16:12058200-12061200	Active TSS	GM12878-XiMat	blood
20	chr16:12058600-12059000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:12058600-12059200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr16:12058600-12059200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:12058600-12059200	Enhancers	Brain Angular Gyrus	brain
24	chr16:12058600-12059200	Enhancers	Brain Hippocampus Middle	brain
25	chr16:12058600-12059400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:12058600-12059400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr16:12058600-12059400	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr16:12058600-12059400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:12058600-12059400	Enhancers	Brain Anterior Caudate	brain
30	chr16:12058600-12059400	Enhancers	Brain Substantia Nigra	brain
31	chr16:12058600-12059800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr16:12058800-12059000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:12058800-12059000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr16:12058800-12059400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:12058800-12059400	Enhancers	NHEK	skin
36	chr16:12058800-12059600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr16:12058800-12059600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr16:12058800-12067600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr16:12058800-12069400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links