Variant report

Variant	rs1469100
Chromosome Location	chr5:52721494-52721495
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	chr11:116036620..116037556-chr5:52721259..52721968,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10805447	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10805448	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10940313	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10940315	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940316	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11738755	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11740067	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11741680	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11742633	0.83[ASN][1000 genomes]
rs11743473	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11744360	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11745102	0.83[ASN][1000 genomes]
rs11745979	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11746341	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11746509	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11746732	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11747948	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11748130	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11748797	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11748901	0.83[ASN][1000 genomes]
rs11955043	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12153379	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153556	0.82[ASN][1000 genomes]
rs12153680	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13153643	0.83[ASN][1000 genomes]
rs13156108	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13162095	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13163048	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13167150	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13169091	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13169122	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13170709	0.84[ASN][1000 genomes]
rs13171352	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13171813	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13174728	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13175176	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13175475	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13176442	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13178720	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13183277	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13188654	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13188772	0.83[ASN][1000 genomes]
rs13189230	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1363971	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423549	0.85[ASN][1000 genomes]
rs1423559	0.85[ASN][1000 genomes]
rs1423561	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34256928	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34437756	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34444043	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34483113	0.83[ASN][1000 genomes]
rs34547502	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34737247	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34744728	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34750307	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34762534	0.82[ASN][1000 genomes]
rs34801686	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34924451	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34942708	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34985749	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35152485	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35201567	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35237162	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35257227	0.83[ASN][1000 genomes]
rs35314846	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35573280	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35581888	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35586638	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35636180	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35930552	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943929	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131065	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4254863	0.83[ASN][1000 genomes]
rs4254864	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4274942	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4279297	0.83[ASN][1000 genomes]
rs4301187	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4326101	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4421065	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4499786	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535418	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4549480	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4568325	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55793310	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55880944	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56285131	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62357814	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62357815	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62357825	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62357827	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62357829	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62357837	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62357857	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62357858	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62357859	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62359260	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62359263	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71592629	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52713800-52722000	Enhancers	NHEK	skin
2	chr5:52713800-52722200	Enhancers	HMEC	breast
3	chr5:52714800-52721600	Enhancers	NHDF-Ad	bronchial
4	chr5:52715400-52723400	Enhancers	Hela-S3	cervix
5	chr5:52716000-52722200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:52718000-52721600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:52718000-52721800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:52718000-52722800	Enhancers	Osteobl	bone
9	chr5:52718200-52721600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:52718200-52721800	Enhancers	NHLF	lung
11	chr5:52718400-52723000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:52719400-52721600	Enhancers	HSMM	muscle
13	chr5:52719400-52722400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:52720000-52721600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:52720000-52725400	Weak transcription	NH-A	brain
16	chr5:52720600-52722800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr5:52720800-52721600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:52720800-52723400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:52721000-52721800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:52721000-52722200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr5:52721000-52722800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr5:52721200-52721800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:52721200-52722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:52721200-52725800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:52721400-52721600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:52721400-52721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:52721400-52722600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:52721400-52722600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:52721400-52723400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:52721400-52725400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:52721400-52725600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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