Variant report

Variant	rs926528
Chromosome Location	chr6:24687999-24688000
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	chr6:24683018..24685866-chr6:24687699..24690360,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1129644	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885208	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056999	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092404	0.80[ASN][1000 genomes]
rs2143337	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143339	0.82[EUR][1000 genomes]
rs2223588	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223589	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181238	0.82[EUR][1000 genomes]
rs3212233	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35178258	0.93[EUR][1000 genomes]
rs3777664	0.80[ASN][1000 genomes]
rs3822901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397216	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712839	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712840	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6931502	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933328	0.80[EUR][1000 genomes]
rs7752101	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764633	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs926528	TDP2	cis	Esophagus Mucosa	GTEx
rs926528	KIAA0319	cis	Whole Blood	GTEx
rs926528	TDP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:71 , 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	chr6:24669000-24690400	Weak transcription	Gastric	stomach
4	chr6:24669000-24693000	Weak transcription	Primary T cells from cord blood	blood
5	chr6:24669000-24701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:24669200-24690800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:24669400-24701600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:24674200-24700000	Weak transcription	Fetal Lung	lung
9	chr6:24674600-24703400	Weak transcription	Aorta	Aorta
10	chr6:24674800-24698200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:24674800-24702200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:24674800-24702200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:24674800-24702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:24676600-24702600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:24678200-24699600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:24678200-24702600	Weak transcription	HSMMtube	muscle
17	chr6:24678800-24701200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:24678800-24701600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:24679400-24700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:24679600-24699800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:24679800-24691800	Weak transcription	Right Ventricle	heart
22	chr6:24680000-24705400	Weak transcription	Colonic Mucosa	Colon
23	chr6:24680600-24702600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:24680800-24701600	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:24681200-24705600	Weak transcription	Ovary	ovary
26	chr6:24681400-24701800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:24682400-24703000	Weak transcription	Lung	lung
28	chr6:24682800-24691000	Weak transcription	Thymus	Thymus
29	chr6:24682800-24699000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:24682800-24701800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:24682800-24702200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:24682800-24702200	Weak transcription	Fetal Stomach	stomach
33	chr6:24683000-24701400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:24683000-24702200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:24684200-24701800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:24684400-24688600	Weak transcription	Fetal Intestine Large	intestine
37	chr6:24684400-24692200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:24684400-24697800	Weak transcription	Fetal Heart	heart
39	chr6:24684400-24699800	Weak transcription	HepG2	liver
40	chr6:24684600-24692800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:24684600-24701200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:24684800-24698800	Weak transcription	K562	blood
43	chr6:24684800-24705400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:24684800-24705600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:24684800-24709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:24685000-24688400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:24685000-24693400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:24685000-24698200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:24685400-24698600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:24685800-24703600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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