Variant report

Variant	rs643890
Chromosome Location	chr13:53427148-53427149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs559234	1.00[AFR][1000 genomes]
rs649506	1.00[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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53426000-53427200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:53426000-53427600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:53426000-53437000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:53426400-53427200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr13:53426400-53427200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr13:53426400-53428400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:53426800-53427200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr13:53426800-53427200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:53426800-53427200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr13:53426800-53428000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr13:53426800-53428200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:53426800-53429200	Enhancers	GM12878-XiMat	blood
13	chr13:53426800-53433800	Weak transcription	Dnd41	blood
14	chr13:53427000-53427200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:53427000-53427200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:53427000-53427200	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr13:53427000-53428200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr13:53427000-53430200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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