Variant report

Variant	rs55939240
Chromosome Location	chr19:36185103-36185104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36184725..36185454-chr19:36281716..36282604,3	K562	blood:
2	chr19:36184372..36185301-chr19:36310613..36311702,6	K562	blood:
3	chr19:36184365..36185469-chr19:36207271..36208713,26	K562	blood:
4	chr19:36184326..36185624-chr19:36206337..36208829,45	MCF-7	breast:
5	chr19:36184634..36185214-chr19:36373087..36373630,2	MCF-7	breast:
6	chr19:36184467..36185236-chr19:36193340..36194279,2	MCF-7	breast:
7	chr19:36184355..36185390-chr19:36422209..36423187,11	K562	blood:
8	chr19:36184431..36185252-chr19:36310666..36311379,3	MCF-7	breast:
9	chr19:36183210..36186350-chr19:36190384..36192650,3	K562	blood:
10	chr19:36184773..36185345-chr19:36228142..36228948,2	MCF-7	breast:
11	chr19:36184398..36185696-chr19:36206796..36208519,15	MCF-7	breast:
12	chr19:35986002..35986928-chr19:36184353..36185285,2	K562	blood:
13	chr19:36184393..36185382-chr19:36422317..36423468,4	MCF-7	breast:
14	chr19:36184588..36185432-chr19:36310650..36311616,2	MCF-7	breast:
15	chr19:36184387..36185171-chr19:36336007..36336944,2	K562	blood:
16	chr19:36183040..36186694-chr19:36206545..36210008,7	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000105663	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000188508	Chromatin interaction
ENSG00000161270	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs107068	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1269214	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs173003	0.82[EUR][1000 genomes]
rs179570	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2242522	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242523	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2285421	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs231238	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs231244	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs231588	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs231591	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs231592	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4806187	0.80[EUR][1000 genomes]
rs61218414	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs614225	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807478	0.81[EUR][1000 genomes]
rs807479	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9917056	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
4	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs55939240	COX6B1	cis	Heart Left Ventricle	GTEx
rs55939240	ZBTB32	cis	Nerve Tibial	GTEx
rs55939240	AC002398.13	cis	Thyroid	GTEx
rs55939240	RN7SL765P	cis	Muscle Skeletal	GTEx
rs55939240	COX6B1	cis	Muscle Skeletal	GTEx
rs55939240	ZBTB32	cis	Thyroid	GTEx
rs55939240	ZBTB32	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36179200-36192800	Weak transcription	Right Atrium	heart
2	chr19:36183000-36193000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:36184200-36185400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:36184400-36185400	Enhancers	Dnd41	blood
5	chr19:36184600-36185200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:36184800-36185400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr19:36184800-36192600	Weak transcription	Placenta	Placenta
8	chr19:36185000-36186000	Enhancers	GM12878-XiMat	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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