Variant report

Variant	rs12229181
Chromosome Location	chr12:121107393-121107394
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	chr12:121086713..121087372-chr12:121107159..121108129,2	MCF-7	breast:
2	chr12:121106092..121108586-chr12:121122971..121126312,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110917	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10431372	1.00[EUR][1000 genomes]
rs10431383	1.00[EUR][1000 genomes]
rs10774564	0.86[ASN][1000 genomes]
rs10774565	0.97[ASN][1000 genomes]
rs10849774	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10849775	0.86[ASN][1000 genomes]
rs10849780	1.00[EUR][1000 genomes]
rs10849781	1.00[EUR][1000 genomes]
rs11065183	0.82[ASN][1000 genomes]
rs11065184	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065186	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065188	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065189	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065191	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065192	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065193	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065194	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065195	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11065196	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065197	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065198	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065199	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065204	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065205	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065214	1.00[EUR][1000 genomes]
rs11065215	1.00[EUR][1000 genomes]
rs11065217	1.00[EUR][1000 genomes]
rs11065220	1.00[EUR][1000 genomes]
rs11065221	1.00[EUR][1000 genomes]
rs11065224	1.00[EUR][1000 genomes]
rs11065229	1.00[EUR][1000 genomes]
rs11065234	1.00[EUR][1000 genomes]
rs11065235	1.00[EUR][1000 genomes]
rs11065238	0.86[EUR][1000 genomes]
rs11065240	0.86[EUR][1000 genomes]
rs11065241	0.86[EUR][1000 genomes]
rs11065242	0.86[EUR][1000 genomes]
rs11065244	1.00[EUR][1000 genomes]
rs11065245	0.86[EUR][1000 genomes]
rs11065246	0.86[EUR][1000 genomes]
rs11065262	0.83[EUR][1000 genomes]
rs12228118	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12228187	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12229164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12231101	0.86[EUR][1000 genomes]
rs12231499	1.00[EUR][1000 genomes]
rs12310160	0.97[ASN][1000 genomes]
rs17848090	1.00[EUR][1000 genomes]
rs2071266	1.00[EUR][1000 genomes]
rs2229534	1.00[EUR][1000 genomes]
rs2239687	1.00[EUR][1000 genomes]
rs2239757	1.00[EUR][1000 genomes]
rs2239759	1.00[EUR][1000 genomes]
rs3751166	1.00[EUR][1000 genomes]
rs3809310	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809311	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7302002	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7973568	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121100000-121107600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:121104400-121108600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:121105800-121107600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr12:121105800-121107600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr12:121105800-121108200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:121105800-121108200	Enhancers	Primary B cells from cord blood	blood
7	chr12:121106000-121107400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:121106000-121107600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:121106000-121109000	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:121106200-121107400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:121106200-121107600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:121106200-121107600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:121106200-121107600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:121106200-121107800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:121106200-121108200	Enhancers	Fetal Intestine Small	intestine
16	chr12:121106400-121107400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr12:121106400-121107400	Enhancers	Fetal Muscle Leg	muscle
18	chr12:121106400-121107800	Enhancers	Brain Hippocampus Middle	brain
19	chr12:121106400-121108000	Enhancers	Fetal Intestine Large	intestine
20	chr12:121106600-121107400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:121106600-121107600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:121106600-121107600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:121106600-121107600	Enhancers	Brain Cingulate Gyrus	brain
24	chr12:121106600-121108200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:121106800-121107400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr12:121106800-121107400	Enhancers	Ovary	ovary
27	chr12:121106800-121107600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:121106800-121107600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr12:121106800-121107600	Enhancers	Stomach Mucosa	stomach
30	chr12:121106800-121107800	Enhancers	Fetal Stomach	stomach
31	chr12:121107000-121107400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:121107000-121107400	Enhancers	Brain Angular Gyrus	brain
33	chr12:121107000-121107400	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr12:121107000-121107400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr12:121107000-121107400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:121107000-121107400	Enhancers	Pancreas	Pancrea
37	chr12:121107000-121107400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr12:121107000-121107400	Enhancers	NH-A	brain
39	chr12:121107000-121107600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:121107000-121107600	Enhancers	Adipose Nuclei	Adipose
41	chr12:121107000-121107600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr12:121107000-121107600	Enhancers	A549	lung
43	chr12:121107000-121107600	Bivalent Enhancer	HepG2	liver
44	chr12:121107000-121107800	Enhancers	NHEK	skin
45	chr12:121107000-121108000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:121107000-121108200	Flanking Active TSS	GM12878-XiMat	blood
47	chr12:121107200-121107400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:121107200-121107400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
49	chr12:121107200-121107400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:121107200-121107400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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