Variant report

Variant	rs58324390
Chromosome Location	chr1:171181754-171181755
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	chr1:171180730..171183096-chr4:189101938..189104230,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10912525	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12064117	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12066662	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12067810	0.91[EUR][1000 genomes]
rs12071595	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12072321	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12078869	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12082112	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12086788	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12087971	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12091865	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13353034	0.83[EUR][1000 genomes]
rs16864136	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16864165	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16864191	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2020860	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2020865	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2205726	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28369826	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369834	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369837	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369850	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369868	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28369872	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28369883	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369886	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28969551	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs29001609	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56060753	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56159716	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56233063	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57182460	0.91[EUR][1000 genomes]
rs58956470	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59910498	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61225278	0.94[EUR][1000 genomes]
rs61233777	0.85[EUR][1000 genomes]
rs6668231	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6673781	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6684218	0.85[EUR][1000 genomes]
rs6689616	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73032526	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74122287	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7527107	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1817255	chr1:171170733-171185865	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171166000-171184000	Weak transcription	Gastric	stomach
2	chr1:171167200-171187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:171169800-171189800	Weak transcription	Right Atrium	heart
4	chr1:171177800-171183600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:171178000-171183200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:171178200-171182600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:171178200-171187200	Weak transcription	Aorta	Aorta
8	chr1:171178600-171182800	Weak transcription	Left Ventricle	heart
9	chr1:171179600-171182200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:171179600-171183000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:171179800-171182200	Weak transcription	Liver	Liver
12	chr1:171179800-171183400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:171179800-171187600	Weak transcription	Brain Substantia Nigra	brain
14	chr1:171179800-171187800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:171180400-171182600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:171180600-171182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:171180600-171182200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:171180600-171187000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:171181000-171182600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:171181000-171187800	Weak transcription	Fetal Lung	lung
21	chr1:171181200-171182200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:171181200-171183200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:171181400-171182400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:171181400-171182600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:171181400-171183200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:171181600-171182000	Weak transcription	Adipose Nuclei	Adipose
27	chr1:171181600-171183200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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