Variant report

Variant	rs11112469
Chromosome Location	chr12:105725635-105725636
allele	C/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	E2F4	chr12:105725346-105725644	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr12:105723677-105726002	IMR90	lung:	n/a	chr12:105724251-105724260
3	POLR2A	chr12:105724922-105725839	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr12:105725174-105726408	SK-N-SH	brain:	n/a	chr12:105725434-105725443
5	RFX5	chr12:105725580-105725748	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr12:105724825-105726056	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAZ	chr12:105723746-105725701	IMR90	lung:	n/a	n/a
8	TCF12	chr12:105725617-105726078	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr12:105723720-105726217	A549	lung:	n/a	n/a
10	PBX3	chr12:105725186-105725805	SK-N-SH	brain:	n/a	chr12:105725434-105725443
11	POLR2A	chr12:105723805-105726031	GM19099	blood:	n/a	n/a
12	SP1	chr12:105725519-105726014	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFYB	chr12:105725253-105725662	GM12878	blood:	n/a	chr12:105725432-105725445
14	SIN3AK20	chr12:105725567-105725940	SK-N-SH	brain:	n/a	n/a
15	WRNIP1	chr12:105725197-105725909	GM12878	blood:	n/a	n/a
16	STAT1	chr12:105725525-105725725	GM12878	blood:	n/a	chr12:105725562-105725570
17	POLR2A	chr12:105724077-105726492	ProgFib	skin:	n/a	n/a
18	FOXA2	chr12:105725509-105725779	HepG2	liver:	n/a	n/a
19	RUNX3	chr12:105724783-105726012	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105720223..105722150-chr12:105723159..105726102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257642	TF binding region
ENSG00000264749	TF binding region
ENSG00000264749	Chromatin interaction
ENSG00000257642	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10507190	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10861400	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861403	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861407	0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10861409	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10861411	0.81[EUR][1000 genomes]
rs10861412	0.81[EUR][1000 genomes]
rs11112465	1.00[CHB][hapmap]
rs11112468	1.00[CHB][hapmap]
rs11112470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112475	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11112478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112480	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112482	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112483	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112484	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112485	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112486	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112487	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112488	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112492	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs11112493	0.81[EUR][1000 genomes]
rs11112498	0.88[CEU][hapmap]
rs11112499	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs12829692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831150	0.84[EUR][1000 genomes]
rs1432592	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17041538	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2888846	0.94[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34189496	0.87[EUR][1000 genomes]
rs34346262	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35325227	0.86[GIH][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35335704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35519603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6797	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7131942	0.81[EUR][1000 genomes]
rs7302174	0.87[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7303242	1.00[CHB][hapmap]
rs7954485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972183	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972676	1.00[CHB][hapmap]
rs9645791	0.88[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11112469	C12orf75	cis	Artery Tibial	GTEx
rs11112469	ANO4	cis	parietal	SCAN
rs11112469	C12orf75	cis	Artery Aorta	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105724000-105725800	Active TSS	Fetal Kidney	kidney
2	chr12:105724000-105725800	Active TSS	Small Intestine	intestine
3	chr12:105724000-105726000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:105724000-105726400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:105724200-105725800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:105724200-105725800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr12:105724200-105725800	Active TSS	Rectal Smooth Muscle	rectum
8	chr12:105724200-105725800	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr12:105724200-105726000	Active TSS	Brain Hippocampus Middle	brain
10	chr12:105724200-105726000	Active TSS	GM12878-XiMat	blood
11	chr12:105724200-105726600	Active TSS	NHDF-Ad	bronchial
12	chr12:105724200-105726800	Active TSS	Aorta	Aorta
13	chr12:105724400-105725800	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr12:105724400-105727800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:105724600-105725800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr12:105724800-105726000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:105725000-105725800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:105725000-105725800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:105725000-105725800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr12:105725000-105726000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:105725000-105726000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:105725000-105726000	Flanking Active TSS	HUVEC	blood vessel
23	chr12:105725000-105726200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr12:105725000-105726200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr12:105725000-105726200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:105725200-105725800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:105725200-105725800	Flanking Active TSS	Fetal Brain Male	brain
28	chr12:105725200-105725800	Enhancers	Lung	lung
29	chr12:105725200-105726000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
30	chr12:105725200-105726000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr12:105725200-105726000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:105725200-105726000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:105725200-105726000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:105725200-105726000	Flanking Active TSS	Hela-S3	cervix
35	chr12:105725200-105726200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:105725200-105726200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr12:105725200-105726200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr12:105725200-105726600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr12:105725200-105727800	Weak transcription	Psoas Muscle	Psoas
40	chr12:105725200-105728600	Enhancers	Placenta	Placenta
41	chr12:105725200-105734600	Weak transcription	Esophagus	oesophagus
42	chr12:105725400-105725800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr12:105725400-105725800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
44	chr12:105725400-105725800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:105725400-105725800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
46	chr12:105725400-105725800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
47	chr12:105725400-105725800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:105725400-105725800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:105725400-105725800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
50	chr12:105725400-105725800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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