Variant report

Variant	rs9316589
Chromosome Location	chr13:53426642-53426643
allele	G/T
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	EP300	chr13:53426558-53426959	SK-N-SH_RA	brain:	n/a	n/a
2	GATA2	chr13:53426562-53427086	SH-SY5Y	brain:	n/a	n/a
3	RUNX3	chr13:53426214-53426722	GM12878	blood:	n/a	chr13:53426603-53426612 chr13:53426603-53426612
4	EP300	chr13:53426585-53426972	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr13:53425526-53427069	SK-N-SH	brain:	n/a	chr13:53426510-53426524 chr13:53426513-53426527 chr13:53426251-53426265 chr13:53426516-53426530 chr13:53426512-53426526
6	GATA3	chr13:53426461-53427099	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:53423777..53426647-chr13:53440227..53445526,5	MCF-7	breast:
2	chr13:53416128..53422445-chr13:53423052..53427915,11	MCF-7	breast:
3	chr13:53424748..53427468-chr13:53541401..53543631,2	MCF-7	breast:
4	chr13:53225548..53228779-chr13:53423444..53428429,4	MCF-7	breast:
5	chr13:53425388..53426892-chr13:53431589..53434414,2	MCF-7	breast:
6	chr13:53226333..53229941-chr13:53424392..53427948,4	MCF-7	breast:
7	chr13:53423269..53426675-chr13:53427472..53433524,8	MCF-7	breast:
8	chr13:53424477..53427390-chr13:53433560..53435155,3	MCF-7	breast:
9	chr13:53419410..53422161-chr13:53423908..53427048,5	MCF-7	breast:
10	chr13:53426133..53429015-chr13:53553120..53555019,2	MCF-7	breast:
11	chr13:53424598..53426748-chr13:53456688..53458919,2	MCF-7	breast:

Variant related genes	Relation type
PCDH8	TF binding region
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs7988815	0.85[AFR][1000 genomes]
rs9316590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9316591	0.85[AFR][1000 genomes]
rs9596694	0.85[AFR][1000 genomes]
rs9596698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596707	0.85[AFR][1000 genomes]

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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900089	chr13:53385334-53429453	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1810064	chr13:53412849-53441018	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1822518	chr13:53412849-53441018	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv1829072	chr13:53412849-53441018	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv523092	chr13:53419139-53429453	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53423800-53426800	Enhancers	Fetal Brain Male	brain
2	chr13:53424400-53426800	Flanking Active TSS	GM12878-XiMat	blood
3	chr13:53425800-53426800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr13:53426000-53426800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr13:53426000-53426800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr13:53426000-53426800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr13:53426000-53426800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr13:53426000-53427200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:53426000-53427600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:53426000-53437000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr13:53426200-53426800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:53426200-53426800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr13:53426200-53426800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr13:53426200-53426800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:53426200-53426800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:53426200-53426800	Enhancers	Fetal Stomach	stomach
17	chr13:53426200-53426800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr13:53426200-53426800	Enhancers	Dnd41	blood
19	chr13:53426200-53427000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr13:53426200-53427000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr13:53426200-53427000	Enhancers	Fetal Muscle Leg	muscle
22	chr13:53426400-53426800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr13:53426400-53426800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr13:53426400-53426800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:53426400-53426800	Enhancers	Fetal Brain Female	brain
26	chr13:53426400-53426800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
27	chr13:53426400-53427000	Enhancers	Brain Germinal Matrix	brain
28	chr13:53426400-53427200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr13:53426400-53427200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr13:53426400-53428400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:53426600-53426800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr13:53426600-53426800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr13:53426600-53426800	Bivalent Enhancer	Fetal Kidney	kidney
34	chr13:53426600-53427000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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