Variant report

Variant	rs559451962
Chromosome Location	chr3:53833710-53833711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53833693-53834938	HepG2	liver:	n/a	n/a
2	CTCF	chr3:53833580-53833730	HBMEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:53833655-53833744	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:53833659-53833815	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53827199..53830305-chr3:53832365..53836212,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271916	TF binding region
ENSG00000157388	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53811400-53838600	Weak transcription	Spleen	Spleen
2	chr3:53811600-53843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53829200-53833800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:53829600-53838200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:53830400-53839800	Weak transcription	Lung	lung
7	chr3:53830400-53851200	Weak transcription	Fetal Brain Male	brain
8	chr3:53830600-53834000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:53830600-53834200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:53830600-53837400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:53830600-53837800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:53830600-53838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:53830600-53838600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:53830600-53838600	Weak transcription	Fetal Brain Female	brain
15	chr3:53830600-53840200	Weak transcription	Brain Angular Gyrus	brain
16	chr3:53830600-53840200	Weak transcription	Pancreas	Pancrea
17	chr3:53830800-53838200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:53830800-53838800	Weak transcription	Brain Anterior Caudate	brain
19	chr3:53830800-53840200	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:53832000-53837400	Strong transcription	Fetal Lung	lung
21	chr3:53832000-53839800	Strong transcription	Fetal Intestine Large	intestine
22	chr3:53832200-53833800	Weak transcription	Fetal Stomach	stomach
23	chr3:53832200-53838800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:53832200-53839800	Strong transcription	Fetal Intestine Small	intestine
25	chr3:53833000-53838400	Weak transcription	Fetal Heart	heart
26	chr3:53833200-53833800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:53833400-53834400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:53833400-53834800	Enhancers	NHDF-Ad	bronchial
29	chr3:53833600-53834400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:53833600-53835000	Enhancers	Esophagus	oesophagus
31	chr3:53833600-53838400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:53833600-53840800	Weak transcription	Fetal Kidney	kidney

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