Variant report

Variant	rs3862447
Chromosome Location	chr16:12089241-12089242
allele	G/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	TAL1	chr16:12089229-12089402	K562	blood:	n/a	n/a
2	ELF1	chr16:12089178-12089449	K562	blood:	n/a	chr16:12089325-12089338

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12068964..12070676-chr16:12088730..12090900,2	MCF-7	breast:
2	chr16:12069104..12071909-chr16:12088073..12090716,2	K562	blood:

Variant related genes	Relation type
SNX29	TF binding region
ENSG00000260488	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000234719	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13332023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13332654	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13334568	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13339152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16958825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16958827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958833	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006256	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869492	0.85[CHB][hapmap]
rs381584	1.00[CHB][hapmap]
rs442332	1.00[CHB][hapmap]
rs448737	1.00[CHB][hapmap]
rs57196125	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7190848	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7199459	1.00[CHB][hapmap]
rs72784609	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052559	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12072000-12093600	Weak transcription	Fetal Stomach	stomach
4	chr16:12072200-12093800	Weak transcription	Thymus	Thymus
5	chr16:12072200-12096600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:12072200-12102600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr16:12072400-12096400	Weak transcription	Ovary	ovary
8	chr16:12072400-12104400	Weak transcription	NHLF	lung
9	chr16:12072600-12094000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:12072600-12094000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:12072600-12099000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr16:12072800-12102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr16:12079600-12109600	Weak transcription	Gastric	stomach
14	chr16:12080200-12090000	Weak transcription	Aorta	Aorta
15	chr16:12080200-12093800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr16:12082000-12091400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr16:12082000-12093000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:12083400-12102800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr16:12084000-12092000	Weak transcription	NHDF-Ad	bronchial
20	chr16:12084800-12091600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:12085200-12090400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
23	chr16:12086600-12090400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr16:12086600-12090600	Weak transcription	Pancreas	Pancrea
25	chr16:12086800-12096600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr16:12087000-12089600	Genic enhancers	GM12878-XiMat	blood
27	chr16:12087000-12090200	Enhancers	Brain Hippocampus Middle	brain
28	chr16:12087200-12089400	Enhancers	Spleen	Spleen
29	chr16:12087200-12089400	Enhancers	HUVEC	blood vessel
30	chr16:12087400-12089400	Enhancers	Brain Cingulate Gyrus	brain
31	chr16:12087400-12092800	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr16:12087800-12089600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr16:12088000-12089600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr16:12088000-12089600	Enhancers	Adipose Nuclei	Adipose
35	chr16:12088000-12089600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr16:12088000-12090200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr16:12088200-12100800	Weak transcription	Fetal Brain Female	brain
38	chr16:12088400-12089400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr16:12088400-12089400	Enhancers	K562	blood
40	chr16:12088400-12090400	Weak transcription	Fetal Thymus	thymus
41	chr16:12088600-12091800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:12088600-12093800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr16:12088600-12098200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr16:12088600-12104200	Weak transcription	Right Ventricle	heart
45	chr16:12088600-12109200	Weak transcription	Fetal Kidney	kidney
46	chr16:12088600-12110000	Weak transcription	NH-A	brain
47	chr16:12088800-12089600	Enhancers	Brain Substantia Nigra	brain
48	chr16:12088800-12090600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr16:12088800-12090800	Weak transcription	HepG2	liver
50	chr16:12088800-12091400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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