Variant report

Variant	rs12539653
Chromosome Location	chr7:129558395-129558396
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:129553929..129555431-chr7:129558253..129560539,2	MCF-7	breast:
2	chr7:129557764..129560612-chr7:129608880..129612426,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs12530557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532959	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533033	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12533528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533953	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12534043	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534061	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534320	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535722	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535728	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12536978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537576	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537604	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537660	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538787	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539145	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539800	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540517	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540541	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12690	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464970	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464971	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464972	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1471877	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17559301	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1965567	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1965568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631601	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2727457	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34930431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35189138	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55732825	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55735840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748031	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55767113	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55769831	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55772531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55798026	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55809128	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56022754	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56025626	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56034137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56080853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56085705	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56094908	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56117230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56153730	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56167610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56176516	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56191413	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56321762	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56332361	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56333543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56376893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56381627	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56408895	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs718925	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs718926	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv831129	chr7:129525406-129702477	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129516200-129584400	Weak transcription	Fetal Brain Male	brain
2	chr7:129518200-129564600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:129530000-129587600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:129541800-129559200	Weak transcription	Esophagus	oesophagus
5	chr7:129544800-129559400	Weak transcription	Lung	lung
6	chr7:129547000-129563600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:129547400-129563600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:129547400-129576800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:129547600-129558400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr7:129548400-129562600	Weak transcription	Hela-S3	cervix
11	chr7:129549200-129586800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:129549400-129580200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:129549800-129572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:129549800-129577800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:129549800-129588200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:129550400-129560800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:129551400-129558600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr7:129552400-129564600	Weak transcription	HMEC	breast
19	chr7:129552800-129563600	Weak transcription	A549	lung
20	chr7:129553000-129559600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr7:129553200-129560000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr7:129553200-129570000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:129553400-129559800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr7:129553400-129560000	Enhancers	Fetal Heart	heart
25	chr7:129554000-129559400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:129554000-129559400	Weak transcription	Gastric	stomach
27	chr7:129554000-129573800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:129554200-129558600	Enhancers	Colon Smooth Muscle	Colon
29	chr7:129554400-129558400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr7:129554400-129559000	Enhancers	Brain Substantia Nigra	brain
31	chr7:129555000-129558600	Weak transcription	Ovary	ovary
32	chr7:129555000-129558800	Enhancers	Primary T cells from cord blood	blood
33	chr7:129555000-129560200	Weak transcription	Osteobl	bone
34	chr7:129555000-129562600	Weak transcription	Fetal Intestine Large	intestine
35	chr7:129555200-129563400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:129555200-129587000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:129555400-129558400	Enhancers	Brain Cingulate Gyrus	brain
38	chr7:129555400-129558600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr7:129555400-129558800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:129555400-129563800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:129555600-129559200	Weak transcription	Thymus	Thymus
42	chr7:129555600-129562600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:129555600-129563200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr7:129555600-129563200	Weak transcription	Stomach Mucosa	stomach
45	chr7:129555600-129563600	Weak transcription	HSMM	muscle
46	chr7:129555600-129564600	Weak transcription	K562	blood
47	chr7:129555800-129558600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:129555800-129559200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:129555800-129559200	Weak transcription	Fetal Thymus	thymus
50	chr7:129555800-129559600	Weak transcription	Duodenum Mucosa	Duodenum

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