Variant report

Variant	rs12539800
Chromosome Location	chr7:129479138-129479139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:129469301..129471027-chr7:129477016..129479280,2	MCF-7	breast:
2	chr7:129468028..129470584-chr7:129477737..129479272,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12530557	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531622	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531936	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532612	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532959	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533033	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533290	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533464	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12533528	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533953	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12534043	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534061	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534320	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535347	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535722	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535857	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12536424	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536978	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537150	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537336	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537576	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537604	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537660	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537782	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12538787	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539145	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539653	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540479	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540517	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540541	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12690	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464970	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464971	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464972	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1471874	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471877	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559301	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965567	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1965568	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631601	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2727457	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34930431	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35189138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55675451	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732825	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55735840	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55748031	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55767113	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55769831	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55772531	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798026	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55809128	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56022754	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025626	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56034137	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56080853	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085705	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56094908	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56117230	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56153730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167610	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56176516	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56191413	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321762	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56332361	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333543	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56376893	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56381627	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56408895	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718926	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129466200-129483800	Weak transcription	Dnd41	blood
2	chr7:129466400-129483400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:129470000-129480400	Weak transcription	Fetal Brain Male	brain
4	chr7:129470400-129480200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:129470400-129480400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:129470400-129480600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:129470400-129480800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:129470400-129480800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:129470400-129483600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:129470600-129480400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:129470600-129480600	Weak transcription	Brain Angular Gyrus	brain
12	chr7:129470800-129480200	Weak transcription	Brain Germinal Matrix	brain
13	chr7:129471200-129479200	Strong transcription	Fetal Stomach	stomach
14	chr7:129471200-129479800	Strong transcription	Primary T cells from cord blood	blood
15	chr7:129471600-129479200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr7:129471600-129479200	Strong transcription	Liver	Liver
17	chr7:129471600-129479400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr7:129471600-129479400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr7:129471600-129479400	Strong transcription	Fetal Thymus	thymus
20	chr7:129471600-129480600	Weak transcription	Brain Substantia Nigra	brain
21	chr7:129472000-129479600	Strong transcription	Primary B cells from cord blood	blood
22	chr7:129472200-129479200	Strong transcription	Fetal Intestine Large	intestine
23	chr7:129472200-129479200	Strong transcription	Fetal Muscle Leg	muscle
24	chr7:129472200-129484200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:129472400-129479400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:129472400-129480200	Weak transcription	Psoas Muscle	Psoas
27	chr7:129472600-129480200	Weak transcription	Pancreas	Pancrea
28	chr7:129472600-129480400	Weak transcription	Right Atrium	heart
29	chr7:129472600-129480800	Weak transcription	A549	lung
30	chr7:129472800-129491400	Weak transcription	Fetal Kidney	kidney
31	chr7:129473000-129479200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr7:129473200-129479200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:129473200-129479200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr7:129473200-129479400	Strong transcription	HSMMtube	muscle
35	chr7:129473400-129479400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:129473600-129479200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:129473600-129479200	Strong transcription	GM12878-XiMat	blood
38	chr7:129473600-129479400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr7:129473600-129479400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr7:129473800-129479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:129473800-129479200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr7:129473800-129479600	Strong transcription	Placenta	Placenta
43	chr7:129474200-129479200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:129474400-129485000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:129474400-129485400	Weak transcription	Small Intestine	intestine
46	chr7:129474800-129479400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:129475000-129479400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr7:129475000-129534800	Weak transcription	Colonic Mucosa	Colon
49	chr7:129475200-129480400	Weak transcription	Fetal Brain Female	brain
50	chr7:129475800-129480000	Weak transcription	HMEC	breast

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