Variant report

Variant	rs12506006
Chromosome Location	chr4:106104097-106104098
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	chr4:106066588..106068608-chr4:106102134..106104288,2	MCF-7	breast:
2	chr4:106064646..106070521-chr4:106098298..106104512,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1114718	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11933960	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12498609	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12511800	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640842	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12642165	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12647779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12647884	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17583579	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17583593	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17616993	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2023841	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088484	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2866774	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533180	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949681	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9637601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
2	chr4:106070400-106107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:106070400-106111600	Weak transcription	Placenta	Placenta
4	chr4:106077000-106112000	Weak transcription	Aorta	Aorta
5	chr4:106078000-106112800	Weak transcription	Fetal Kidney	kidney
6	chr4:106080600-106105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:106080600-106107800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:106083600-106109200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:106083800-106104800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:106083800-106111400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:106084000-106105000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
13	chr4:106085600-106112800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:106086000-106105600	Weak transcription	Fetal Lung	lung
15	chr4:106090400-106105600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:106090600-106107000	Weak transcription	NH-A	brain
17	chr4:106092000-106105800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:106092000-106110600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:106093800-106111200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr4:106093800-106112400	Weak transcription	Primary B cells from cord blood	blood
21	chr4:106094000-106112600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:106096200-106111600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:106096400-106111200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:106096600-106107200	Weak transcription	Psoas Muscle	Psoas
25	chr4:106097400-106105800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:106097600-106105600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr4:106098000-106111400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:106098200-106113200	Weak transcription	Fetal Stomach	stomach
29	chr4:106099000-106114200	Weak transcription	Gastric	stomach
30	chr4:106100800-106108000	Weak transcription	Osteobl	bone
31	chr4:106101000-106105800	Weak transcription	Left Ventricle	heart
32	chr4:106101000-106146600	Weak transcription	Spleen	Spleen
33	chr4:106101200-106105200	Weak transcription	Small Intestine	intestine
34	chr4:106101200-106105600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:106101200-106112600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:106101200-106112800	Weak transcription	NHDF-Ad	bronchial
37	chr4:106101400-106104800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:106101400-106105400	Weak transcription	HepG2	liver
39	chr4:106101400-106105800	Weak transcription	Adipose Nuclei	Adipose
40	chr4:106101400-106112200	Weak transcription	Right Atrium	heart
41	chr4:106101600-106105400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:106101600-106112800	Weak transcription	HSMM	muscle
43	chr4:106101800-106105800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:106102000-106105800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:106102000-106107200	Weak transcription	Ovary	ovary
46	chr4:106102200-106105400	Weak transcription	Liver	Liver
47	chr4:106102200-106105800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:106102200-106107800	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:106102400-106105600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:106102400-106105800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links