Variant report

Variant	rs12306541
Chromosome Location	chr12:72668176-72668177
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	CTCF	chr12:72668100-72668250	HBMEC	blood vessel:	n/a	n/a
2	CHD1	chr12:72664483-72669298	IMR90	lung:	n/a	chr12:72665403-72665413 chr12:72666399-72666409
3	MXI1	chr12:72664946-72668220	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:72664308..72665953-chr12:72666174..72668987,2	MCF-7	breast:

Variant related genes	Relation type
TRHDE-AS1	TF binding region
TRHDE	TF binding region
ENSG00000236333	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10506649	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179134	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300104	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12318344	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319940	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110963	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4312105	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350401	0.85[ASN][1000 genomes]
rs4394875	0.85[ASN][1000 genomes]
rs4558203	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137961	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313633	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969488	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7969786	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv559362	chr12:72641784-72694691	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72663000-72668400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:72663200-72670200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:72663200-72671200	Active TSS	NH-A	brain
4	chr12:72663400-72669400	Active TSS	Right Atrium	heart
5	chr12:72665000-72668200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:72665000-72668200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:72665000-72668600	Bivalent/Poised TSS	Osteobl	bone
8	chr12:72665200-72668200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:72665800-72668800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
10	chr12:72665800-72671400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:72666000-72668200	Bivalent Enhancer	Fetal Brain Male	brain
12	chr12:72666000-72668200	Bivalent/Poised TSS	Fetal Brain Female	brain
13	chr12:72666200-72668200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
14	chr12:72666400-72668200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr12:72666600-72668200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
16	chr12:72667000-72668200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
17	chr12:72667000-72668200	Bivalent/Poised TSS	Psoas Muscle	Psoas
18	chr12:72667000-72669000	Active TSS	Pancreas	Pancrea
19	chr12:72667200-72668800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
20	chr12:72667400-72668200	Bivalent/Poised TSS	Colonic Mucosa	Colon
21	chr12:72667400-72668800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
22	chr12:72667400-72668800	Bivalent/Poised TSS	Fetal Kidney	kidney
23	chr12:72667600-72668200	Bivalent/Poised TSS	NHDF-Ad	bronchial
24	chr12:72667600-72668400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
25	chr12:72667800-72668200	Bivalent Enhancer	Esophagus	oesophagus
26	chr12:72667800-72668200	Flanking Active TSS	Ovary	ovary
27	chr12:72667800-72668400	Flanking Active TSS	Liver	Liver
28	chr12:72667800-72668400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
29	chr12:72667800-72668600	Weak transcription	Aorta	Aorta
30	chr12:72667800-72668600	Flanking Active TSS	HMEC	breast
31	chr12:72667800-72668800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:72667800-72668800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr12:72667800-72671400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:72667800-72671400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:72668000-72668200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr12:72668000-72668200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:72668000-72668200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:72668000-72668200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:72668000-72668200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
40	chr12:72668000-72668200	Bivalent Enhancer	Brain Germinal Matrix	brain
41	chr12:72668000-72668200	Active TSS	Brain Substantia Nigra	brain
42	chr12:72668000-72668200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr12:72668000-72668200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr12:72668000-72668400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
45	chr12:72668000-72668400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
46	chr12:72668000-72668400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
47	chr12:72668000-72668400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:72668000-72668600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:72668000-72668600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
50	chr12:72668000-72668800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain

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