Variant report

Variant	rs12758546
Chromosome Location	chr1:114223635-114223636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114222809..114226325-chr1:114228244..114229950,3	K562	blood:
2	chr1:113933524..113935646-chr1:114221508..114224251,2	MCF-7	breast:
3	chr1:113933102..113934672-chr1:114222696..114225562,2	MCF-7	breast:
4	chr1:114221190..114223803-chr1:114226200..114229279,3	MCF-7	breast:
5	chr1:114222246..114224526-chr1:114245061..114247466,2	K562	blood:
6	chr1:114223041..114225984-chr1:114230466..114232583,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10127930	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10489936	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1080307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217384	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12723023	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729708	0.82[EUR][1000 genomes]
rs12730675	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12730735	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12731010	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12731969	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12734625	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12735104	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12739970	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12746609	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12748727	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12752932	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12753075	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12753351	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12760457	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13374352	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17274550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17274620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17274634	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17462614	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17508163	0.82[ASN][1000 genomes]
rs17508814	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17509390	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1885454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040040	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2359173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2359174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34042871	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34258372	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34341173	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34649199	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34698891	0.92[EUR][1000 genomes]
rs34799402	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34857922	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34877889	0.87[EUR][1000 genomes]
rs35320278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35383900	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35836713	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36115604	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3747998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752953	0.84[EUR][1000 genomes]
rs3761931	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789595	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789607	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3789609	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4581284	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55855422	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56257513	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61817579	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61817586	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61817617	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61819423	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61819424	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61820162	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668829	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6674848	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66782936	0.84[ASN][1000 genomes]
rs6703387	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7533391	0.82[EUR][1000 genomes]
rs7533605	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7549685	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7555354	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9803891	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
2	chr1:114173000-114226800	Weak transcription	Aorta	Aorta
3	chr1:114173800-114236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:114179800-114239600	Weak transcription	Spleen	Spleen
5	chr1:114183000-114235800	Weak transcription	Dnd41	blood
6	chr1:114185200-114224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:114185400-114228000	Weak transcription	HepG2	liver
8	chr1:114196600-114226400	Weak transcription	Gastric	stomach
9	chr1:114200200-114227800	Weak transcription	Stomach Mucosa	stomach
10	chr1:114202000-114241400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:114203000-114232000	Weak transcription	Fetal Brain Female	brain
12	chr1:114203000-114237800	Weak transcription	NH-A	brain
13	chr1:114203200-114224800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:114203200-114232200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:114203200-114237600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
17	chr1:114203400-114237800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:114206600-114226400	Weak transcription	NHLF	lung
19	chr1:114206600-114229800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:114207400-114230600	Weak transcription	NHEK	skin
21	chr1:114209600-114229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:114209800-114232400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:114211200-114231400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:114211600-114234600	Weak transcription	Brain Germinal Matrix	brain
25	chr1:114213400-114225400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:114213600-114232000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:114213600-114241600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:114214800-114232400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:114215000-114226800	Weak transcription	Ovary	ovary
30	chr1:114215400-114235800	Weak transcription	Esophagus	oesophagus
31	chr1:114215400-114235800	Weak transcription	Lung	lung
32	chr1:114216000-114247000	Weak transcription	HMEC	breast
33	chr1:114216200-114225800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:114216200-114241600	Weak transcription	Pancreas	Pancrea
35	chr1:114216200-114279800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:114216400-114232000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:114216400-114250400	Weak transcription	Placenta	Placenta
38	chr1:114216600-114225600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:114216600-114225600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:114216600-114227600	Weak transcription	Fetal Thymus	thymus
41	chr1:114216800-114226400	Weak transcription	Primary T cells from cord blood	blood
42	chr1:114217200-114224800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:114217800-114226000	Weak transcription	Fetal Stomach	stomach
44	chr1:114218000-114235800	Weak transcription	Psoas Muscle	Psoas
45	chr1:114218200-114224400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:114218200-114225600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:114218200-114227400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:114218200-114240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:114218400-114223800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:114218800-114225800	Weak transcription	Primary monocytes fromperipheralblood	blood

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