Variant report

Variant	rs12330534
Chromosome Location	chr3:51672455-51672456
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51535498..51537200-chr3:51671383..51672799,10	MCF-7	breast:
2	chr3:51670498..51672609-chr3:51704591..51706589,2	MCF-7	breast:
3	chr3:51671896..51672809-chr3:51715723..51716758,4	K562	blood:
4	chr3:51533880..51536429-chr3:51670590..51673480,2	K562	blood:
5	chr3:51533551..51537019-chr3:51670604..51674164,6	MCF-7	breast:
6	chr3:51535149..51536784-chr3:51671586..51672589,18	MCF-7	breast:
7	chr3:51671983..51672502-chr3:51716007..51716637,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164081	Chromatin interaction
ENSG00000145041	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs13314120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13321674	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13325153	1.00[CHB][hapmap];0.94[YRI][hapmap]
rs13433729	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051832	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	1.00[AMR][1000 genomes]
rs28653367	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2883900	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	1.00[AMR][1000 genomes]
rs56942057	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951441	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	1.00[AMR][1000 genomes]
rs9827917	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	1.00[AMR][1000 genomes]
rs9842066	1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	1.00[AMR][1000 genomes]
rs9864213	1.00[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880050	1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880909	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882601	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51655800-51680200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:51656000-51673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:51660800-51680200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:51660800-51681000	Strong transcription	HepG2	liver
5	chr3:51660800-51681400	Strong transcription	Primary T cells from cord blood	blood
6	chr3:51660800-51681800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:51660800-51683000	Strong transcription	Primary B cells from cord blood	blood
8	chr3:51660800-51683200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:51661000-51676600	Strong transcription	Adipose Nuclei	Adipose
10	chr3:51661000-51679600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:51661000-51680200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:51661000-51680400	Strong transcription	Dnd41	blood
13	chr3:51661000-51682600	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:51661000-51682600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:51661000-51682600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:51661000-51683000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:51661000-51684200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:51661200-51680600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:51661200-51680600	Strong transcription	Thymus	Thymus
20	chr3:51661200-51681200	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:51661200-51681800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:51661200-51682600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:51661200-51683000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr3:51661200-51683000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:51661400-51680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:51661400-51681200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:51661400-51681800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:51661400-51681800	Strong transcription	Lung	lung
29	chr3:51661400-51682600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:51661400-51682600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:51661400-51682800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr3:51661400-51683000	Strong transcription	Brain Hippocampus Middle	brain
33	chr3:51661600-51676400	Strong transcription	Fetal Brain Female	brain
34	chr3:51661600-51679800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:51661600-51681600	Strong transcription	Fetal Stomach	stomach
36	chr3:51661600-51681800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:51661600-51682000	Strong transcription	Fetal Thymus	thymus
38	chr3:51661600-51682600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:51661600-51682600	Strong transcription	Brain Anterior Caudate	brain
40	chr3:51661600-51683200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:51661600-51683200	Strong transcription	Left Ventricle	heart
42	chr3:51661800-51675800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:51661800-51683200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:51662000-51683000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:51662200-51674400	Strong transcription	Fetal Intestine Small	intestine
46	chr3:51662600-51681800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:51662600-51682600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:51662800-51680400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:51662800-51681200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:51662800-51682400	Strong transcription	Brain Cingulate Gyrus	brain

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