Variant report

Variant	rs2046929
Chromosome Location	chr12:40495632-40495633
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40481786..40484578-chr12:40492831..40495668,2	MCF-7	breast:
2	12:40491106-40496076..12:40793507-40812339	GM12878	blood:
3	chr12:40480723..40487168-chr12:40489659..40495663,7	K562	blood:
4	chr12:40494859..40496427-chr12:40496570..40499467,2	MCF-7	breast:
5	chr12:40419862..40422582-chr12:40493466..40495715,2	K562	blood:
6	12:40491106-40496076..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction
ENSG00000205592	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10506145	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1086490	1.00[JPT][hapmap]
rs10877837	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11174370	1.00[JPT][hapmap]
rs11564133	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11564137	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11564139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11564160	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564194	1.00[JPT][hapmap]
rs11564223	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564282	1.00[JPT][hapmap]
rs12312535	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371119	1.00[JPT][hapmap]
rs12810368	1.00[JPT][hapmap]
rs12827948	1.00[JPT][hapmap]
rs1482282	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1491926	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17442108	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17442304	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17442469	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442756	1.00[JPT][hapmap]
rs17442805	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17443112	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17458299	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17458396	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17458403	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17461082	1.00[CHB][hapmap]
rs17461492	1.00[AFR][1000 genomes]
rs17465400	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17465519	0.92[AFR][1000 genomes]
rs17465540	0.92[AFR][1000 genomes]
rs17483628	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559478	1.00[JPT][hapmap]
rs2086598	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2404346	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404574	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2708404	1.00[JPT][hapmap]
rs28370607	0.82[ASN][1000 genomes]
rs28370611	0.82[ASN][1000 genomes]
rs28370644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370654	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370656	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28370659	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370681	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28740188	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55707305	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55993200	1.00[AFR][1000 genomes]
rs7305377	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7306718	1.00[JPT][hapmap]
rs7484475	1.00[JPT][hapmap]
rs7969495	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974522	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7974972	1.00[JPT][hapmap]
rs992851	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1816874	chr12:40492814-40499934	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
5	esv1822895	chr12:40492814-40499934	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
6	esv1838004	chr12:40492814-40499934	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
7	esv1841992	chr12:40492814-40499934	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
8	esv1850635	chr12:40492814-40499934	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
9	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1839896	chr12:40493591-40499908	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40466400-40498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40471400-40496800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:40474400-40497000	Weak transcription	Ovary	ovary
4	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:40475600-40496400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:40476400-40497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:40476600-40498400	Weak transcription	Fetal Stomach	stomach
8	chr12:40476800-40497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:40477000-40497000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:40477400-40496800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:40480600-40496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:40482000-40497800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:40485600-40496800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:40487000-40497400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr12:40488200-40498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:40491000-40497000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:40492400-40498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:40492800-40496800	Weak transcription	Pancreas	Pancrea
19	chr12:40492800-40497600	Weak transcription	Left Ventricle	heart
20	chr12:40492800-40498000	Weak transcription	Gastric	stomach
21	chr12:40492800-40498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:40492800-40498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:40492800-40498600	Weak transcription	Lung	lung
24	chr12:40493000-40496600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:40493600-40495800	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:40493600-40496800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:40493600-40497000	Weak transcription	Brain Anterior Caudate	brain
28	chr12:40493600-40497000	Weak transcription	Fetal Kidney	kidney
29	chr12:40493800-40497400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:40493800-40497400	Weak transcription	Fetal Heart	heart
31	chr12:40494000-40496800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:40494000-40496800	Weak transcription	HepG2	liver
33	chr12:40494000-40497000	Weak transcription	Liver	Liver
34	chr12:40494000-40497000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:40494200-40495800	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr12:40494200-40496000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:40494200-40496600	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:40494200-40496800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:40494200-40496800	Weak transcription	Fetal Intestine Small	intestine
40	chr12:40494200-40496800	Enhancers	K562	blood
41	chr12:40494200-40498000	Weak transcription	Fetal Lung	lung
42	chr12:40494200-40498200	Weak transcription	A549	lung
43	chr12:40494400-40495800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr12:40494400-40496600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:40494400-40496800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:40494400-40497000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:40494600-40496800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:40494600-40497000	Weak transcription	Stomach Mucosa	stomach
49	chr12:40494600-40498000	Weak transcription	NHLF	lung
50	chr12:40495200-40495800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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