Variant report

Variant	rs13249102
Chromosome Location	chr8:58944300-58944301
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	chr8:58943502..58945075-chr8:58945226..58947971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253523	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10086632	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10089240	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10091875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10099623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504246	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1105302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108188	0.81[CHB][hapmap]
rs11780747	0.81[CHB][hapmap]
rs11783171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11998684	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs12114333	0.82[EUR][1000 genomes]
rs13252750	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13279262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34915140	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35124619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35856042	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4407868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4524775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4524776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930039	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56128341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57650783	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58124183	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60265023	0.87[EUR][1000 genomes]
rs6994434	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999606	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7009526	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7017824	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7826402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828423	0.81[CHB][hapmap]
rs7841308	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7841370	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7842565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297984	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv831324	chr8:58844151-59045309	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:58924400-58946400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr8:58927000-58948000	Weak transcription	Fetal Brain Male	brain
3	chr8:58929400-58944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:58935000-58948600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:58935000-58950200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:58935600-58988800	Weak transcription	Aorta	Aorta
7	chr8:58936200-58944600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr8:58936400-58945200	Weak transcription	Fetal Kidney	kidney
9	chr8:58941400-58944600	Enhancers	Colon Smooth Muscle	Colon
10	chr8:58941600-58944400	Weak transcription	Lung	lung
11	chr8:58941600-58944400	Weak transcription	Spleen	Spleen
12	chr8:58941800-58946200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr8:58941800-58946400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr8:58942400-58945800	Weak transcription	Fetal Intestine Large	intestine
15	chr8:58942600-58945000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr8:58942800-58944400	Weak transcription	Fetal Brain Female	brain
17	chr8:58943000-58944600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:58943200-58945400	Enhancers	HepG2	liver
19	chr8:58943200-58948200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr8:58943200-58950400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr8:58943400-58944400	Weak transcription	Fetal Intestine Small	intestine
22	chr8:58943400-58945400	Enhancers	Pancreas	Pancrea
23	chr8:58943600-58944600	Enhancers	Stomach Mucosa	stomach
24	chr8:58943600-58944800	Enhancers	Gastric	stomach
25	chr8:58943600-58945400	Enhancers	Liver	Liver
26	chr8:58943800-58944400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr8:58943800-58944400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr8:58943800-58944600	Enhancers	Ovary	ovary
29	chr8:58943800-58944800	Genic enhancers	Fetal Muscle Leg	muscle
30	chr8:58943800-58945000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr8:58943800-58946600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr8:58943800-58949600	Weak transcription	Placenta	Placenta
33	chr8:58943800-58950000	Weak transcription	Adipose Nuclei	Adipose
34	chr8:58943800-58951200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:58944000-58944400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr8:58944000-58944600	Weak transcription	Psoas Muscle	Psoas
37	chr8:58944000-58944600	Weak transcription	HSMM	muscle
38	chr8:58944000-58945000	Weak transcription	Brain Germinal Matrix	brain
39	chr8:58944000-58946400	Weak transcription	Brain Hippocampus Middle	brain
40	chr8:58944000-58946400	Weak transcription	Left Ventricle	heart
41	chr8:58944000-58946400	Weak transcription	Right Atrium	heart
42	chr8:58944000-58946400	Weak transcription	Right Ventricle	heart
43	chr8:58944000-58949400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr8:58944000-58950200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr8:58944000-58950200	Weak transcription	Brain Substantia Nigra	brain
46	chr8:58944000-58950200	Weak transcription	HSMMtube	muscle
47	chr8:58944000-58950400	Weak transcription	Brain Anterior Caudate	brain
48	chr8:58944000-58950400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr8:58944000-58951400	Weak transcription	NHLF	lung
50	chr8:58944000-58951600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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