Variant report

Variant	rs1558039
Chromosome Location	chr7:108072029-108072030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108066256..108068604-chr7:108069393..108073824,4	K562	blood:
2	chr7:108069636..108072852-chr7:108078819..108081993,4	MCF-7	breast:
3	chr7:108067231..108072750-chr7:108078077..108081806,4	K562	blood:
4	chr7:108069523..108074084-chr7:108075336..108078341,6	MCF-7	breast:
5	chr7:108059629..108061203-chr7:108069537..108072425,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10235291	0.87[EUR][1000 genomes]
rs10239916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10240397	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10241916	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10241941	0.97[EUR][1000 genomes]
rs10264851	0.97[EUR][1000 genomes]
rs10264905	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10278718	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10280579	0.97[EUR][1000 genomes]
rs1116335	0.97[EUR][1000 genomes]
rs12705468	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1558037	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2158849	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2160555	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2395964	0.89[EUR][1000 genomes]
rs2395996	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2395997	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2395998	0.97[EUR][1000 genomes]
rs2395999	0.97[EUR][1000 genomes]
rs4727711	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730310	0.97[EUR][1000 genomes]
rs4730311	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730312	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730313	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4730314	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730315	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730316	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730317	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730319	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6466227	0.97[EUR][1000 genomes]
rs6466228	0.97[EUR][1000 genomes]
rs6466229	0.97[EUR][1000 genomes]
rs6466230	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6466231	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6466232	0.97[EUR][1000 genomes]
rs6944286	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6948610	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6973727	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6975183	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7780552	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7782059	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7787736	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7788503	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7792379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7799296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9656149	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs970660	0.95[AMR][1000 genomes];0.94[EUR][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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108059800-108073400	Weak transcription	Fetal Brain Female	brain
2	chr7:108067600-108081000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:108067800-108089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:108068000-108089400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:108069000-108086000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:108069600-108074400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:108070000-108072200	Genic enhancers	A549	lung
8	chr7:108070800-108074200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:108071000-108072600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:108071200-108072200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr7:108071200-108072600	Enhancers	Pancreas	Pancrea
12	chr7:108071800-108074400	Weak transcription	HUVEC	blood vessel
13	chr7:108071800-108074800	Weak transcription	Brain Anterior Caudate	brain
14	chr7:108071800-108075200	Weak transcription	HMEC	breast
15	chr7:108072000-108074800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:108072000-108075800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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