Variant report

Variant	rs7972912
Chromosome Location	chr12:121283293-121283294
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120727503..120731222-chr12:121282952..121285914,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10849804	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11065208	0.85[JPT][hapmap]
rs11065211	0.85[JPT][hapmap]
rs11065212	0.85[JPT][hapmap]
rs11065230	0.85[JPT][hapmap]
rs11065270	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11065278	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11065295	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11065314	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11829904	0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11833718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12296423	0.85[JPT][hapmap]
rs12306138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533810	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1533811	0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4559761	0.85[JPT][hapmap]
rs59757908	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60238091	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61523086	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6489783	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6490302	0.85[JPT][hapmap]
rs695950	0.85[JPT][hapmap]
rs7133413	1.00[ASW][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7301612	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7303170	0.85[JPT][hapmap]
rs7307973	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7309538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7316132	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7316417	0.88[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7956848	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7958698	0.85[JPT][hapmap]
rs7960336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs949443	0.85[JPT][hapmap]

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	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	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
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121267600-121285800	Weak transcription	Colonic Mucosa	Colon
2	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
3	chr12:121272800-121285600	Weak transcription	Hela-S3	cervix
4	chr12:121274000-121284000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:121274000-121285800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:121274000-121287200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:121274200-121291800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:121274400-121284800	Weak transcription	Primary B cells from cord blood	blood
9	chr12:121274400-121285200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:121274400-121285200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:121274400-121285400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:121274400-121285400	Weak transcription	Aorta	Aorta
13	chr12:121274400-121285800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:121274400-121289400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:121274600-121285200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:121274600-121289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:121274600-121289800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:121274800-121284600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:121274800-121291800	Weak transcription	Dnd41	blood
20	chr12:121275000-121284600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:121275000-121284600	Weak transcription	Fetal Lung	lung
22	chr12:121277600-121287200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:121278200-121283600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:121279200-121289200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:121279400-121284000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:121279400-121286400	Enhancers	Brain Substantia Nigra	brain
27	chr12:121279600-121286600	Enhancers	Brain Hippocampus Middle	brain
28	chr12:121279800-121284000	Enhancers	Brain Anterior Caudate	brain
29	chr12:121280200-121284600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:121280400-121283400	Enhancers	Pancreas	Pancrea
31	chr12:121280800-121284000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:121280800-121284000	Enhancers	Ovary	ovary
33	chr12:121280800-121284400	Weak transcription	HSMM	muscle
34	chr12:121280800-121287400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:121281000-121283600	Enhancers	Right Atrium	heart
36	chr12:121281000-121284200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:121281200-121283600	Enhancers	Fetal Thymus	thymus
38	chr12:121281200-121284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:121281400-121283400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr12:121281400-121284200	Enhancers	Left Ventricle	heart
41	chr12:121281400-121284600	Weak transcription	HSMMtube	muscle
42	chr12:121281400-121285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:121281600-121283800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr12:121281600-121296200	Weak transcription	HepG2	liver
45	chr12:121281800-121286000	Enhancers	Colon Smooth Muscle	Colon
46	chr12:121282000-121286400	Enhancers	Right Ventricle	heart
47	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
48	chr12:121282200-121283400	Enhancers	Adipose Nuclei	Adipose
49	chr12:121282200-121283600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr12:121282200-121283800	Genic enhancers	Spleen	Spleen

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