Variant report

Variant	rs4308054
Chromosome Location	chr19:52054601-52054602
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52054537..52061127-chr19:52066145..52073451,11	K562	blood:
2	chr19:51970702..51973310-chr19:52051081..52054707,4	K562	blood:
3	chr19:52036245..52040151-chr19:52052262..52055120,4	K562	blood:
4	chr19:52054163..52056571-chr19:52069054..52071841,3	K562	blood:
5	chr19:52053557..52056461-chr19:52303271..52305092,2	K562	blood:
6	chr19:52053867..52056450-chr19:52073512..52076767,3	K562	blood:
7	chr19:52005076..52007479-chr19:52052391..52054693,2	K562	blood:
8	chr19:51963894..51965992-chr19:52053600..52057338,3	K562	blood:

No data

No data

No data

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1125620	0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1379284	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1585160	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs16982846	0.90[ASN][1000 genomes]
rs17453522	0.84[JPT][hapmap]
rs1962189	0.85[JPT][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2305371	0.84[JPT][hapmap]
rs2864106	0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2864109	0.90[ASN][1000 genomes]
rs3752129	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs3752132	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6509552	0.84[JPT][hapmap]
rs7245838	0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7249641	0.91[ASN][1000 genomes]
rs8102214	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8108872	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs8111685	0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4308054	ZNF175	cis	Esophagus Mucosa	GTEx
rs4308054	ZNF175	cis	Esophagus Muscularis	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52048800-52058000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:52052800-52056400	Weak transcription	Spleen	Spleen
3	chr19:52053400-52054800	Active TSS	K562	blood
4	chr19:52053600-52054800	Weak transcription	Primary T cells from cord blood	blood
5	chr19:52053600-52056400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr19:52054000-52057000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr19:52054200-52055000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr19:52054400-52055600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:52054600-52054800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:52054600-52055000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:52054600-52055400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
12	chr19:52054600-52055400	Flanking Active TSS	GM12878-XiMat	blood
13	chr19:52054600-52055600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr19:52054600-52056800	Flanking Active TSS	Primary B cells from peripheral blood	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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