Variant report

Variant	rs62378245
Chromosome Location	chr5:88743962-88743963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16867571	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16867576	0.93[AFR][1000 genomes]
rs66580221	0.93[AFR][1000 genomes]
rs6891794	0.93[AFR][1000 genomes]
rs7701188	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532159	chr5:88016214-88783092	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv533373	chr5:88062497-89028098	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv529543	chr5:88348147-88783092	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv830388	chr5:88578939-88793870	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv598927	chr5:88647766-88780868	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv830389	chr5:88669984-88860383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv882357	chr5:88677293-88774328	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
8	nsv882358	chr5:88677293-88776034	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
9	nsv882359	chr5:88710519-88785384	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
10	nsv882360	chr5:88716714-88785384	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
11	esv1845994	chr5:88736275-88847756	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr5:88739400-88752000	Enhancers	Primary B cells from peripheral blood	blood
2	chr5:88740400-88744800	Enhancers	Primary B cells from cord blood	blood
3	chr5:88740800-88752400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:88741600-88745400	Weak transcription	GM12878-XiMat	blood
5	chr5:88742000-88744400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr5:88742600-88746600	Enhancers	Brain Germinal Matrix	brain
7	chr5:88743000-88744400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:88743000-88744400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:88743000-88745600	Enhancers	Fetal Brain Male	brain
10	chr5:88743200-88744200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:88743200-88744400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr5:88743200-88744400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:88743200-88745600	Enhancers	Fetal Brain Female	brain
14	chr5:88743200-88746200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:88743400-88744200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr5:88743400-88744600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr5:88743600-88744000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr5:88743600-88744000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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

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