Variant report

Variant	rs12228854
Chromosome Location	chr12:48396920-48396921
allele	G/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	MAX	chr12:48396421-48397087	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
2	SUZ12	chr12:48396098-48398262	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr12:48395778-48397117	MCF-7	breast:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
4	HA-E2F1	chr12:48395990-48397009	MCF-7	breast:	n/a	n/a
5	NRF1	chr12:48396003-48397082	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr12:48396800-48396950	HPAF	blood vessel:	n/a	n/a
7	SETDB1	chr12:48396415-48397021	U2OS	brain:	n/a	n/a
8	MAX	chr12:48396433-48396935	HepG2	liver:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
9	MAX	chr12:48396791-48397050	H1-hESC	embryonic stem cell:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
10	CTCF	chr12:48396780-48396930	MCF-7	breast:	n/a	n/a
11	KAP1	chr12:48394655-48397087	HEK293	kidney:	n/a	n/a
12	TCF12	chr12:48396360-48397034	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr12:48395799-48397245	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
14	KAP1	chr12:48396036-48397040	U2OS	brain:	n/a	n/a
15	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a
16	MXI1	chr12:48394606-48397189	SK-N-SH	brain:	n/a	n/a
17	MAX	chr12:48396319-48397210	ECC-1	luminal epithelium:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
18	MAX	chr12:48396431-48397042	HepG2	liver:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
19	MAX	chr12:48394712-48397112	ECC-1	luminal epithelium:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48396876-48396883 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48396875-48396884 chr12:48394939-48394948 chr12:48395771-48395781 chr12:48396872-48396887
20	CTCF	chr12:48396820-48396970	AG09319	gingival:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48355944..48359601-chr12:48393326..48397759,4	MCF-7	breast:
2	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:
3	chr12:48394829..48397203-chr12:48403090..48404738,2	MCF-7	breast:
4	chr12:48295052..48296721-chr12:48395942..48397721,2	MCF-7	breast:
5	chr12:48393252..48397718-chr12:48414474..48419166,5	MCF-7	breast:
6	chr12:48342574..48344961-chr12:48394535..48396923,2	MCF-7	breast:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000134291	Chromatin interaction
ENSG00000139219	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10875714	0.89[EUR][1000 genomes]
rs10875715	0.86[EUR][1000 genomes]
rs10875750	0.82[YRI][hapmap]
rs11168355	0.82[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs11168357	0.82[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs11168369	0.82[YRI][hapmap]
rs11168414	0.82[YRI][hapmap]
rs11168427	0.82[YRI][hapmap]
rs11168433	0.82[YRI][hapmap]
rs12304476	0.82[YRI][hapmap]
rs12305511	0.82[LWK][hapmap]
rs12306451	0.82[YRI][hapmap]
rs12308909	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12721420	0.85[CEU][hapmap]
rs17122666	0.82[YRI][hapmap]
rs1990028	1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs2213162	0.95[CHB][hapmap]
rs2213163	0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2226946	0.94[CHB][hapmap]
rs2228500	0.82[YRI][hapmap]
rs2269935	0.82[YRI][hapmap]
rs2269936	0.82[YRI][hapmap]
rs2898056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737548	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3782910	0.82[YRI][hapmap]
rs3782915	0.89[EUR][1000 genomes]
rs3809322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809324	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760609	0.85[TSI][hapmap]
rs4760695	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs56037230	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56959315	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs740022	0.89[EUR][1000 genomes]
rs886588	0.82[YRI][hapmap]
rs989144	0.82[YRI][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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12228854	FAM186B	cis	parietal	SCAN
rs12228854	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs12228854	LOC255411	cis	cerebellum	SCAN
rs12228854	RP1-228P16.1	cis	Thyroid	GTEx
rs12228854	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12228854	LMBR1L	cis	cerebellum	SCAN
rs12228854	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs12228854	SENP1	cis	parietal	SCAN
rs12228854	ZNF641	cis	Muscle Skeletal	GTEx
rs12228854	PRPF40B	cis	parietal	SCAN
rs12228854	ASB8	cis	cerebellum	SCAN
rs12228854	ARID2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48394800-48397000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
2	chr12:48394800-48397200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
3	chr12:48394800-48397800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:48394800-48397800	Enhancers	Spleen	Spleen
5	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
6	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
7	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:48395000-48397000	Active TSS	Aorta	Aorta
9	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
10	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
11	chr12:48395000-48398000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:48395000-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
13	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
14	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
18	chr12:48395200-48397600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
19	chr12:48395200-48398200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
20	chr12:48395200-48398600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
21	chr12:48395200-48398800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:48395400-48397800	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr12:48395400-48398600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
24	chr12:48395400-48398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:48395600-48397000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
26	chr12:48395600-48397000	Flanking Active TSS	Ovary	ovary
27	chr12:48395600-48397200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:48395600-48397200	Bivalent Enhancer	Small Intestine	intestine
29	chr12:48395600-48398000	Flanking Bivalent TSS/Enh	HepG2	liver
30	chr12:48395600-48398400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:48395600-48399000	Enhancers	Pancreas	Pancrea
32	chr12:48395800-48397000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
33	chr12:48395800-48397000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
34	chr12:48395800-48397000	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
35	chr12:48395800-48397400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
36	chr12:48395800-48397800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
37	chr12:48395800-48398400	Enhancers	Lung	lung
38	chr12:48395800-48399200	Bivalent/Poised TSS	Fetal Kidney	kidney
39	chr12:48396000-48397000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
40	chr12:48396000-48397000	Bivalent Enhancer	Fetal Brain Male	brain
41	chr12:48396000-48397000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:48396000-48397000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr12:48396000-48397000	Flanking Active TSS	Right Ventricle	heart
44	chr12:48396000-48397000	Flanking Bivalent TSS/Enh	NHEK	skin
45	chr12:48396000-48397200	Flanking Bivalent TSS/Enh	A549	lung
46	chr12:48396000-48397800	Bivalent Enhancer	Esophagus	oesophagus
47	chr12:48396000-48398000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:48396000-48398000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr12:48396000-48398000	Enhancers	Gastric	stomach
50	chr12:48396200-48397400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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