Variant report

Variant	rs7962695
Chromosome Location	chr12:48029718-48029719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48014490..48017395-chr12:48029451..48031685,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10492007	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17122136	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17122138	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2100808	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36123489	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4348981	0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4550297	0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56915320	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56967344	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57671593	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58292976	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58702884	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59702452	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60739072	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60873325	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61702904	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs716665	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7298221	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7303895	0.94[YRI][hapmap]
rs7304743	0.94[YRI][hapmap]
rs7311790	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7315257	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298686	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298687	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298689	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73300611	0.89[AMR][1000 genomes]
rs73300632	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300647	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300650	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300653	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300658	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73300663	1.00[AMR][1000 genomes]
rs73300666	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300680	1.00[AMR][1000 genomes]
rs748306	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7964752	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs877196	1.00[MEX][hapmap]
rs877197	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv558786	chr12:47942029-48044011	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv527728	chr12:47954597-48044506	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3419735	chr12:48025385-48030183	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7962695	RPAP3	cis	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47998800-48030800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:48007400-48041800	Weak transcription	HSMMtube	muscle
3	chr12:48007400-48044800	Weak transcription	Aorta	Aorta
4	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:48007600-48032000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:48007600-48037600	Weak transcription	Left Ventricle	heart
7	chr12:48008600-48033400	Weak transcription	Pancreas	Pancrea
8	chr12:48009000-48032200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:48009800-48036200	Weak transcription	Ovary	ovary
10	chr12:48014800-48030600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:48015600-48055200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:48016000-48044400	Weak transcription	NH-A	brain
13	chr12:48018000-48036800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:48018800-48030600	Weak transcription	Fetal Stomach	stomach
15	chr12:48020800-48029800	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:48023000-48030400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:48023600-48044800	Weak transcription	Gastric	stomach
18	chr12:48024800-48030600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:48025000-48030800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:48025200-48036000	Weak transcription	Fetal Lung	lung
21	chr12:48025600-48032000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:48025600-48032200	Weak transcription	Primary T cells from cord blood	blood
23	chr12:48025800-48029800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:48025800-48030600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:48025800-48032400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:48027000-48030000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr12:48028000-48031600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:48028400-48030600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:48028600-48030600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:48028800-48030600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:48028800-48031400	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr12:48029000-48031400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
33	chr12:48029000-48031600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:48029200-48031000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:48029400-48030200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:48029400-48030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:48029400-48030400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:48029400-48030600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:48029400-48030800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:48029400-48030800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:48029400-48055400	Weak transcription	Thymus	Thymus
42	chr12:48029600-48030000	Weak transcription	Primary B cells from cord blood	blood
43	chr12:48029600-48030400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:48029600-48030600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:48029600-48030600	Weak transcription	A549	lung

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