Variant report

Variant	rs56328407
Chromosome Location	chr3:85012755-85012756
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	chr3:85011548..85014009-chr3:85014905..85018347,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17022263	1.00[AMR][1000 genomes]
rs41425244	1.00[AMR][1000 genomes]
rs56152547	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60728740	1.00[AMR][1000 genomes]
rs6770335	1.00[EUR][1000 genomes]
rs73843248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73843249	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73843250	1.00[AMR][1000 genomes]
rs73843251	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73843255	1.00[AMR][1000 genomes]
rs73843257	1.00[AMR][1000 genomes]
rs73843259	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73843260	1.00[AMR][1000 genomes]
rs73843263	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73845111	1.00[AMR][1000 genomes]
rs73845113	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85011200-85013400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:85011200-85016600	Weak transcription	Psoas Muscle	Psoas
3	chr3:85011200-85016800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr3:85011200-85016800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:85011600-85016800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:85011600-85016800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:85011600-85018400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:85011800-85013800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:85011800-85013800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:85011800-85013800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:85011800-85014200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:85011800-85014400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:85012000-85013000	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:85012000-85013000	Active TSS	Fetal Brain Female	brain
15	chr3:85012000-85016800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:85012200-85012800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:85012200-85012800	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr3:85012200-85012800	Enhancers	Brain Substantia Nigra	brain
19	chr3:85012200-85012800	Enhancers	Fetal Brain Male	brain
20	chr3:85012400-85014000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:85012400-85014400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:85012600-85012800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:85012600-85013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:85012600-85014200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:85012600-85014400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:85012600-85014400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:85012600-85014400	Enhancers	Brain Hippocampus Middle	brain
28	chr3:85012600-85014400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:85012600-85014600	Weak transcription	Brain Angular Gyrus	brain

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