Variant report

Variant	rs11172336
Chromosome Location	chr12:58177292-58177293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58165508..58166165-chr12:58176772..58177339,2	MCF-7	breast:
2	chr12:58086909..58089805-chr12:58175888..58177930,2	K562	blood:
3	chr12:58175489..58177867-chr12:58239241..58240765,2	MCF-7	breast:
4	chr12:58176542..58178155-chr12:58239377..58241593,2	K562	blood:
5	chr12:58176052..58177919-chr12:58192741..58195580,2	MCF-7	breast:
6	chr12:58176803..58178403-chr12:58230455..58233005,2	K562	blood:
7	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
8	chr12:58177143..58179601-chr12:58187871..58190318,2	K562	blood:
9	chr12:58146595..58149356-chr12:58175469..58178051,2	K562	blood:
10	chr12:58176873..58178429-chr12:58205054..58207229,2	MCF-7	breast:
11	chr12:58175049..58178042-chr12:58240093..58242141,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139266	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000257953	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000123427	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11172322	0.83[YRI][hapmap]
rs11172325	0.83[YRI][hapmap]
rs11172339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11172340	0.82[AFR][1000 genomes]
rs11172348	0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11555555	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11829917	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12297574	0.83[AMR][1000 genomes]
rs12297635	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12297639	1.00[AMR][1000 genomes]
rs12321371	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1389302	1.00[AMR][1000 genomes]
rs3473	0.83[YRI][hapmap]
rs8176348	0.88[ASW][hapmap];0.83[AMR][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	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11172336	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58176000-58177400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:58176000-58177400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:58176200-58177400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:58176200-58177400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:58176200-58177400	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:58176200-58177400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:58176200-58177400	Active TSS	Psoas Muscle	Psoas
8	chr12:58176200-58177400	Active TSS	Right Atrium	heart
9	chr12:58176200-58177400	Active TSS	NHDF-Ad	bronchial
10	chr12:58176200-58177600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:58176200-58177600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:58176200-58177800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:58176400-58177400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:58176400-58177400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:58176400-58177400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:58176400-58177400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:58176400-58177400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:58176400-58177400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:58176400-58177400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr12:58176400-58177400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:58176400-58177400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:58176400-58177400	Active TSS	Esophagus	oesophagus
23	chr12:58176400-58177400	Active TSS	Fetal Intestine Large	intestine
24	chr12:58176400-58177400	Active TSS	Left Ventricle	heart
25	chr12:58176400-58177400	Active TSS	Lung	lung
26	chr12:58176400-58177400	Active TSS	Ovary	ovary
27	chr12:58176400-58177400	Active TSS	Pancreas	Pancrea
28	chr12:58176400-58177600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr12:58176400-58177600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr12:58176400-58177600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:58176400-58177600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:58176400-58177600	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:58176400-58177600	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr12:58176400-58177600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:58176400-58177600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:58176400-58177600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:58176400-58177600	Active TSS	GM12878-XiMat	blood
38	chr12:58176400-58177600	Active TSS	K562	blood
39	chr12:58176400-58177800	Active TSS	A549	lung
40	chr12:58176400-58177800	Active TSS	Hela-S3	cervix
41	chr12:58176400-58177800	Active TSS	HSMM	muscle
42	chr12:58176400-58178000	Active TSS	NHLF	lung
43	chr12:58176600-58177400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:58176600-58177400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
45	chr12:58176600-58177400	Bivalent/Poised TSS	HepG2	liver
46	chr12:58176600-58177600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:58176600-58178200	Transcr. at gene 5' and 3'	Dnd41	blood
48	chr12:58176800-58177400	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr12:58176800-58177400	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr12:58176800-58177400	Flanking Active TSS	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links