Variant report

Variant	rs11172113
Chromosome Location	chr12:57527283-57527284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57526711-57527345	U87	brain:	n/a	n/a
2	FOXA1	chr12:57526962-57527312	HepG2	liver:	n/a	n/a
3	MAZ	chr12:57525540-57528414	IMR90	lung:	n/a	n/a
4	TEAD4	chr12:57527000-57527483	ECC-1	luminal epithelium:	n/a	n/a
5	RCOR1	chr12:57526149-57527414	IMR90	lung:	n/a	n/a
6	TEAD4	chr12:57526999-57527510	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOXA1	chr12:57526987-57527335	HepG2	liver:	n/a	n/a
8	TEAD4	chr12:57527005-57527409	HepG2	liver:	n/a	n/a
9	TEAD4	chr12:57527081-57527421	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOXA2	chr12:57526905-57527312	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57520108..57523293-chr12:57525745..57528597,4	MCF-7	breast:
2	chr12:57520290..57524994-chr12:57525334..57528665,7	K562	blood:
3	chr12:57521171..57523110-chr12:57526141..57527809,2	MCF-7	breast:
4	chr12:57525779..57529405-chr12:57538402..57541799,3	MCF-7	breast:
5	chr12:57526158..57527957-chr12:57535916..57537889,2	MCF-7	breast:

No data

Variant related genes	Relation type
STAT6	TF binding region
ENSG00000259125	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10876964	0.87[ASN][1000 genomes]
rs10876965	0.87[ASN][1000 genomes]
rs12298170	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs12322902	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs1466535	1.00[JPT][hapmap]
rs4367982	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs4759044	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4759275	0.81[TSI][hapmap];0.82[YRI][hapmap]
rs4759276	0.84[CEU][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes]
rs4759277	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

Variant related diseases (count:7)

Disease	PMID	Source
Pulmonary function (interaction)	23284291	GWAS catalog
Migraine without aura	23793025	GWAS catalog
Migraine	21666692	GWAS catalog
Migraine	23793025	GWAS catalog
Migraine	22683712	GWAS catalog
Migraine - clinic-based	23793025	GWAS catalog
Pulmonary function	21946350	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11172113	SP1	cis	cerebellum	SCAN
rs11172113	KIF5A	cis	cerebellum	SCAN
rs11172113	ATP5B	cis	cerebellum	SCAN
rs11172113	STAT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57523000-57530400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:57523400-57557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:57523600-57528200	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr12:57523600-57529600	Enhancers	A549	lung
5	chr12:57523600-57532400	Weak transcription	Pancreas	Pancrea
6	chr12:57523800-57527400	Flanking Active TSS	NH-A	brain
7	chr12:57523800-57529600	Enhancers	Stomach Mucosa	stomach
8	chr12:57523800-57530000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:57523800-57530600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:57523800-57532600	Weak transcription	Gastric	stomach
11	chr12:57523800-57537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:57524000-57527400	Enhancers	Aorta	Aorta
13	chr12:57524000-57528200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr12:57524000-57530400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr12:57524000-57530400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:57524000-57542200	Weak transcription	HMEC	breast
17	chr12:57524000-57543000	Weak transcription	NHEK	skin
18	chr12:57524400-57529200	Genic enhancers	Fetal Stomach	stomach
19	chr12:57524400-57530000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:57524600-57529400	Enhancers	Placenta	Placenta
21	chr12:57524600-57530400	Enhancers	Left Ventricle	heart
22	chr12:57524800-57530600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:57524800-57530800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:57525000-57527800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr12:57525200-57529400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr12:57525200-57529800	Enhancers	Duodenum Mucosa	Duodenum
27	chr12:57525400-57529400	Genic enhancers	Fetal Intestine Small	intestine
28	chr12:57525600-57528200	Enhancers	Fetal Heart	heart
29	chr12:57525800-57529200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr12:57525800-57529400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:57525800-57531800	Weak transcription	Small Intestine	intestine
32	chr12:57525800-57534200	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:57526000-57528000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:57526000-57528400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:57526000-57530400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:57526000-57531000	Enhancers	Brain Angular Gyrus	brain
37	chr12:57526200-57527600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:57526200-57528200	Flanking Active TSS	Osteobl	bone
39	chr12:57526200-57534800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:57526400-57527800	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr12:57526400-57527800	Flanking Active TSS	NHLF	lung
42	chr12:57526400-57528000	Weak transcription	Esophagus	oesophagus
43	chr12:57526400-57528000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr12:57526400-57528200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:57526400-57528400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:57526400-57528400	Enhancers	Colonic Mucosa	Colon
47	chr12:57526400-57528800	Enhancers	Brain Substantia Nigra	brain
48	chr12:57526400-57529000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr12:57526400-57529200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:57526400-57529400	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links