Variant report

Variant	rs2472649
Chromosome Location	chr4:74857708-74857709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
PPBP	TF binding region
ENSG00000163737	Chromatin interaction
ENSG00000163735	Chromatin interaction
ENSG00000163736	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11729931	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12505025	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512838	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13118512	0.86[EUR][1000 genomes]
rs13136948	0.83[CEU][hapmap]
rs1435521	0.83[CEU][hapmap]
rs2115693	0.85[EUR][1000 genomes]
rs4694655	1.00[ASW][hapmap];0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Inflammatory bowel disease	23128233	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2472649	GC	cis	cerebellum	SCAN
rs2472649	CXCL5	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74848600-74863000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:74850400-74862800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:74850800-74863000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:74852000-74862800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:74852000-74863000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:74856600-74861800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:74856600-74863200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:74857000-74858400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:74857200-74858200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:74857400-74858200	Enhancers	Primary hematopoietic stem cells short term culture	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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