Variant report

Variant	rs3782699
Chromosome Location	chr12:106637876-106637877
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106634944..106646449-chr12:106667585..106679535,27	MCF-7	breast:
2	chr12:106636406..106639904-chr12:106695865..106698141,3	MCF-7	breast:
3	chr12:106637683..106639757-chr12:106691523..106693781,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166046	Chromatin interaction
ENSG00000136026	Chromatin interaction
ENSG00000238609	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10459209	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs10507209	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs11112908	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148413	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1148415	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1148417	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1148419	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs1148421	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs1148422	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs1215740	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs1215741	0.91[ASN][1000 genomes]
rs1215757	0.84[ASN][1000 genomes]
rs1215759	0.84[ASN][1000 genomes]
rs1215761	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs1215807	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs12227822	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12231439	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1237262	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs1238021	0.82[ASN][1000 genomes]
rs2649718	0.89[ASN][1000 genomes]
rs3088113	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741882	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61942136	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830730	chr12:106621530-106642222	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv1839947	chr12:106622186-106642064	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv1797996	chr12:106622186-106642222	Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv560055	chr12:106634722-106641710	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv560056	chr12:106634722-106642064	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv560057	chr12:106634722-106642170	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv560058	chr12:106634722-106642222	Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv560059	chr12:106637876-106641962	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv1792778	chr12:106637876-106642222	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv1842648	chr12:106637876-106642222	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv560060	chr12:106637876-106642390	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	esv1799917	chr12:106637876-106649988	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv1834434	chr12:106637876-106649988	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106621400-106638200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:106622200-106639000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:106622200-106639600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:106625200-106640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:106628600-106638600	Weak transcription	Fetal Brain Male	brain
6	chr12:106629000-106638400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:106629400-106639000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:106630200-106638600	Weak transcription	Hela-S3	cervix
9	chr12:106630200-106638600	Strong transcription	NHLF	lung
10	chr12:106630400-106638200	Strong transcription	HSMM	muscle
11	chr12:106630600-106638600	Weak transcription	Small Intestine	intestine
12	chr12:106631400-106638400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:106631400-106638600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:106631600-106638400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:106631800-106638400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:106632200-106638200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:106632800-106639000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:106633200-106638400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:106633400-106638800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:106633400-106638800	Weak transcription	GM12878-XiMat	blood
21	chr12:106633600-106638000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:106633600-106639000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:106634000-106638000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:106634000-106638800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:106634000-106638800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:106634000-106638800	Weak transcription	Brain Anterior Caudate	brain
27	chr12:106634000-106638800	Weak transcription	Brain Substantia Nigra	brain
28	chr12:106634000-106639600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:106634200-106638000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:106634200-106638200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:106634200-106638400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:106634200-106638800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:106634200-106638800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:106634200-106638800	Weak transcription	Brain Angular Gyrus	brain
35	chr12:106634200-106638800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:106634200-106639000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:106634200-106639000	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:106634200-106639600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:106634200-106639800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr12:106634200-106639800	Weak transcription	Fetal Intestine Small	intestine
41	chr12:106634200-106640200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:106634200-106640600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:106634200-106640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:106634400-106639000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:106634800-106638400	Weak transcription	Colonic Mucosa	Colon
46	chr12:106634800-106638600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:106635400-106638200	Genic enhancers	Left Ventricle	heart
48	chr12:106635400-106638200	Strong transcription	HMEC	breast
49	chr12:106635400-106638400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:106635600-106639800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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