Variant report

Variant	rs12240
Chromosome Location	chr16:31439170-31439171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31438153..31440436-chr16:31470611..31472702,2	K562	blood:
2	chr16:31438871..31441365-chr16:31452629..31455736,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260267	Chromatin interaction
ENSG00000176723	Chromatin interaction
ENSG00000140691	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11863886	1.00[CHB][hapmap]
rs2454907	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2454909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2454911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8056156	0.95[AFR][1000 genomes]
rs9931651	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
5	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
6	nsv1066280	chr16:31396464-31452067	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
8	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
9	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
10	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
11	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
12	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
13	esv3402863	chr16:31437451-31439449	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12240	KCTD13	cis	parietal	SCAN
rs12240	IL27	cis	cerebellum	SCAN
rs12240	CD2BP2	cis	parietal	SCAN
rs12240	MAPK3	cis	parietal	SCAN
rs12240	SNORA30	cis	cerebellum	SCAN
rs12240	NUPR1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31437400-31439200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr16:31437600-31439200	Enhancers	Fetal Heart	heart
3	chr16:31438600-31439200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
4	chr16:31438600-31439200	Enhancers	Primary hematopoietic stem cells	blood
5	chr16:31438600-31439200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr16:31438600-31439200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr16:31438600-31439200	Enhancers	Fetal Kidney	kidney
8	chr16:31438600-31439200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
9	chr16:31438600-31439200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr16:31438600-31439200	Enhancers	Spleen	Spleen
11	chr16:31438600-31439400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:31438600-31439600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:31438600-31439600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr16:31438600-31439800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr16:31438600-31439800	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr16:31438600-31440000	Active TSS	Liver	Liver
17	chr16:31438600-31440000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr16:31438800-31439200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:31438800-31439200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr16:31438800-31439200	Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr16:31438800-31439200	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr16:31438800-31439200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr16:31438800-31439200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr16:31438800-31439200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
25	chr16:31438800-31439200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
26	chr16:31438800-31439200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:31438800-31439200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr16:31438800-31439200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr16:31438800-31439200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr16:31438800-31439200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr16:31438800-31439200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr16:31438800-31439200	Bivalent Enhancer	Fetal Brain Male	brain
33	chr16:31438800-31439200	Flanking Active TSS	HMEC	breast
34	chr16:31438800-31439200	Enhancers	K562	blood
35	chr16:31438800-31439200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr16:31438800-31439400	Bivalent Enhancer	Fetal Stomach	stomach
37	chr16:31438800-31439600	Active TSS	Brain Hippocampus Middle	brain
38	chr16:31438800-31439600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr16:31438800-31439600	Active TSS	Brain Substantia Nigra	brain
40	chr16:31438800-31439600	Enhancers	Esophagus	oesophagus
41	chr16:31438800-31439600	Enhancers	Gastric	stomach
42	chr16:31438800-31439600	Enhancers	Lung	lung
43	chr16:31438800-31439600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr16:31438800-31439600	Enhancers	Small Intestine	intestine
45	chr16:31438800-31439600	Active TSS	HSMM	muscle
46	chr16:31438800-31439800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr16:31438800-31439800	Active TSS	Brain Anterior Caudate	brain
48	chr16:31438800-31439800	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr16:31438800-31439800	Active TSS	Fetal Brain Female	brain
50	chr16:31438800-31439800	Active TSS	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links