Variant report

Variant	rs9937428
Chromosome Location	chr16:12394854-12394855
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	EP300	chr16:12394709-12395264	SK-N-SH_RA	brain:	n/a	n/a
2	TCF12	chr16:12394242-12395185	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr16:12394198-12395335	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr16:12394200-12395335	SK-N-SH	brain:	n/a	n/a
5	EP300	chr16:12394718-12395352	SK-N-SH_RA	brain:	n/a	n/a
6	YY1	chr16:12394808-12395209	SK-N-SH_RA	brain:	n/a	n/a
7	PBX3	chr16:12394291-12395202	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000238685	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs56361711	1.00[AMR][1000 genomes]
rs8063836	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9940325	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12338200-12396200	Weak transcription	Thymus	Thymus
2	chr16:12347800-12395200	Weak transcription	Right Ventricle	heart
3	chr16:12359800-12418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
5	chr16:12373400-12414200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr16:12373600-12396600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr16:12374000-12397400	Weak transcription	Ovary	ovary
8	chr16:12374200-12417200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:12383200-12407800	Weak transcription	Gastric	stomach
10	chr16:12384400-12409000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr16:12385000-12396400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr16:12385400-12399200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr16:12385800-12410800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr16:12386400-12401600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr16:12388000-12398600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr16:12388400-12395200	Weak transcription	Pancreas	Pancrea
17	chr16:12388600-12408200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr16:12389800-12397400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:12389800-12398400	Weak transcription	NHEK	skin
20	chr16:12389800-12398800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:12391200-12397200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr16:12391200-12397600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr16:12393800-12395000	Enhancers	Colon Smooth Muscle	Colon
24	chr16:12393800-12395200	Enhancers	Rectal Smooth Muscle	rectum
25	chr16:12393800-12396200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:12393800-12397800	Strong transcription	GM12878-XiMat	blood
27	chr16:12394000-12395000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr16:12394000-12395000	Enhancers	Fetal Stomach	stomach
29	chr16:12394000-12395200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr16:12394000-12395600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:12394000-12396600	Strong transcription	Primary T cells from cord blood	blood
32	chr16:12394200-12395200	Enhancers	Brain Hippocampus Middle	brain
33	chr16:12394200-12395400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr16:12394200-12395400	Enhancers	Brain Angular Gyrus	brain
35	chr16:12394200-12395400	Enhancers	Brain Cingulate Gyrus	brain
36	chr16:12394200-12395600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr16:12394200-12395600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr16:12394200-12396200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr16:12394400-12395000	Strong transcription	Liver	Liver
40	chr16:12394400-12395000	Enhancers	HMEC	breast
41	chr16:12394400-12395200	Enhancers	Brain Substantia Nigra	brain
42	chr16:12394400-12395600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:12394400-12395600	Enhancers	Stomach Smooth Muscle	stomach
44	chr16:12394400-12395800	Enhancers	Brain Anterior Caudate	brain
45	chr16:12394400-12396000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr16:12394400-12396000	Strong transcription	Adipose Nuclei	Adipose
47	chr16:12394400-12396800	Strong transcription	Primary B cells from cord blood	blood
48	chr16:12394400-12396800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr16:12394600-12395200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr16:12394600-12395200	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links