Variant report

Variant	rs4712839
Chromosome Location	chr6:24686291-24686292
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24596221..24598717-chr6:24684990..24687804,2	MCF-7	breast:
2	chr6:24685636..24687384-chr6:24694298..24696772,2	K562	blood:
3	chr6:24578930..24581415-chr6:24684398..24686867,2	K562	blood:

Variant related genes	Relation type
ENSG00000218186	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1053598	0.82[EUR][1000 genomes]
rs10946719	0.87[EUR][1000 genomes]
rs1129644	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555086	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555087	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555088	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885208	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885209	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885210	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1923188	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2056999	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092404	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2143337	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223588	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223589	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212233	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777664	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3822901	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4397216	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4712840	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6931502	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933328	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7752101	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7764633	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770027	0.83[EUR][1000 genomes]
rs926528	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926529	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461049	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4712839	TDP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24668200-24699800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:24668800-24691800	Weak transcription	Psoas Muscle	Psoas
3	chr6:24669000-24686400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:24669000-24690400	Weak transcription	Gastric	stomach
5	chr6:24669000-24693000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:24669000-24701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:24669200-24690800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:24669400-24687600	Weak transcription	Left Ventricle	heart
9	chr6:24669400-24701600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr6:24671400-24687200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:24674200-24700000	Weak transcription	Fetal Lung	lung
12	chr6:24674600-24703400	Weak transcription	Aorta	Aorta
13	chr6:24674800-24698200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:24674800-24702200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:24674800-24702200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:24674800-24702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:24676600-24702600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:24678200-24699600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:24678200-24702600	Weak transcription	HSMMtube	muscle
20	chr6:24678800-24687000	Weak transcription	Placenta	Placenta
21	chr6:24678800-24701200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:24678800-24701600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:24679400-24700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:24679600-24699800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:24679800-24691800	Weak transcription	Right Ventricle	heart
26	chr6:24680000-24705400	Weak transcription	Colonic Mucosa	Colon
27	chr6:24680600-24702600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:24680800-24701600	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:24681200-24686600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:24681200-24687400	Weak transcription	Liver	Liver
31	chr6:24681200-24705600	Weak transcription	Ovary	ovary
32	chr6:24681400-24701800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:24682400-24703000	Weak transcription	Lung	lung
34	chr6:24682600-24687200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:24682800-24687400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:24682800-24691000	Weak transcription	Thymus	Thymus
37	chr6:24682800-24699000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:24682800-24701800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:24682800-24702200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:24682800-24702200	Weak transcription	Fetal Stomach	stomach
41	chr6:24683000-24701400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:24683000-24702200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:24683200-24687200	Weak transcription	Primary B cells from cord blood	blood
44	chr6:24684200-24687200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:24684200-24701800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:24684400-24688600	Weak transcription	Fetal Intestine Large	intestine
47	chr6:24684400-24692200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:24684400-24697800	Weak transcription	Fetal Heart	heart
49	chr6:24684400-24699800	Weak transcription	HepG2	liver
50	chr6:24684600-24687000	Weak transcription	Fetal Intestine Small	intestine

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