Variant report

Variant	rs1569198
Chromosome Location	chr10:54076271-54076272
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	SP1	chr10:54075739-54076499	A549	lung:	n/a	n/a
2	POLR2A	chr10:54075749-54077050	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:54073615-54076920	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr10:54075834-54076630	HepG2	liver:	n/a	n/a
5	POLR2A	chr10:54073525-54079363	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr10:54073092-54080655	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr10:54075719-54077043	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr10:54074915-54076802	HCT-116	colon:	n/a	n/a
9	HEY1	chr10:54073574-54076765	HepG2	liver:	n/a	n/a
10	GATA3	chr10:54072834-54077297	SK-N-SH	brain:	n/a	chr10:54076036-54076046 chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
11	GATA2	chr10:54075864-54077059	HUVEC	blood vessel:	n/a	chr10:54076036-54076046
12	GATA3	chr10:54075696-54077006	SK-N-SH	brain:	n/a	chr10:54076036-54076046
13	POLR2A	chr10:54072864-54080901	ProgFib	skin:	n/a	n/a
14	BCL3	chr10:54074833-54076941	A549	lung:	n/a	chr10:54074906-54074919 chr10:54074911-54074920
15	POLR2A	chr10:54074945-54078566	HepG2	liver:	n/a	n/a
16	TAF1	chr10:54073206-54076883	A549	lung:	n/a	n/a
17	REST	chr10:54075559-54076380	A549	lung:	n/a	chr10:54075680-54075700 chr10:54075680-54075700
18	POLR2A	chr10:54072740-54080656	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr10:54073229-54079826	HUVEC	blood vessel:	n/a	n/a
20	TCF12	chr10:54072631-54080026	A549	lung:	n/a	n/a
21	USF1	chr10:54073324-54077167	A549	lung:	n/a	chr10:54074078-54074094
22	POLR2A	chr10:54076250-54076562	Gliobla	brain:	n/a	n/a
23	POLR2A	chr10:54072772-54079176	HCT-116	colon:	n/a	n/a
24	POLR2A	chr10:54073363-54076907	MCF-7	breast:	n/a	n/a
25	POLR2A	chr10:54072679-54080064	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr10:54075620-54079910	MCF10A-Er-Src	breast:	n/a	n/a
27	ZNF217	chr10:54075907-54076854	MCF-7	breast:	n/a	n/a
28	POLR2A	chr10:54072716-54080807	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
2	chr10:54075650..54077950-chr10:54331128..54333518,2	MCF-7	breast:
3	chr10:54075288..54077844-chr10:54220203..54222382,2	MCF-7	breast:
4	chr10:54068229..54070730-chr10:54076005..54078630,2	K562	blood:
5	chr10:54075730..54077425-chr10:54167077..54169136,2	MCF-7	breast:
6	chr10:54073396..54076476-chr10:54227833..54231095,3	MCF-7	breast:
7	chr10:54073032..54076598-chr10:54229475..54234592,10	MCF-7	breast:
8	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:
9	chr10:54068768..54071357-chr10:54075695..54080723,4	MCF-7	breast:

Variant related genes	Relation type
PRKG1-AS1	TF binding region
ENSG00000231131	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11001584	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11815201	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1528877	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1569199	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv895400	chr10:54073294-54094359	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1569198	PRKG1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54073400-54076600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:54073600-54077000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr10:54074200-54077000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr10:54074400-54077400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr10:54074800-54076400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:54074800-54076400	Active TSS	Placenta	Placenta
7	chr10:54074800-54076600	Active TSS	Fetal Kidney	kidney
8	chr10:54074800-54077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:54074800-54078000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:54074800-54078000	Weak transcription	Spleen	Spleen
11	chr10:54075000-54076600	Flanking Active TSS	Hela-S3	cervix
12	chr10:54075000-54076800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:54075000-54076800	Transcr. at gene 5' and 3'	NHEK	skin
14	chr10:54075000-54078000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:54075000-54078400	Transcr. at gene 5' and 3'	A549	lung
16	chr10:54075200-54077400	Transcr. at gene 5' and 3'	HMEC	breast
17	chr10:54075400-54078200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr10:54075600-54077400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:54075600-54077400	Transcr. at gene 5' and 3'	Osteobl	bone
20	chr10:54075600-54078000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr10:54075800-54076800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:54075800-54076800	Transcr. at gene 5' and 3'	NHLF	lung
23	chr10:54075800-54077000	Transcr. at gene 5' and 3'	HSMM	muscle
24	chr10:54075800-54077200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:54075800-54077600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:54075800-54077600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:54075800-54078200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
28	chr10:54076000-54076400	Active TSS	HSMMtube	muscle
29	chr10:54076000-54076600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:54076000-54076600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr10:54076000-54076600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:54076000-54077000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:54076000-54077200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
34	chr10:54076200-54076400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:54076200-54076400	Enhancers	HepG2	liver
36	chr10:54076200-54076600	Transcr. at gene 5' and 3'	NH-A	brain
37	chr10:54076200-54077200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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