Variant report

Variant	rs246797
Chromosome Location	chr5:75647630-75647631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2055440	0.82[EUR][1000 genomes]
rs246795	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2937728	0.83[EUR][1000 genomes]
rs2937729	0.81[EUR][1000 genomes]
rs2937730	0.81[EUR][1000 genomes]
rs2937731	0.81[EUR][1000 genomes]
rs2972841	0.81[EUR][1000 genomes]
rs405030	1.00[CHB][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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv870415	chr5:75526088-75738412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1023310	chr5:75609686-75651786	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020853	chr5:75611597-75651786	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3326642	chr5:75636096-75647694	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs246797	SPZ1	cis	parietal	SCAN
rs246797	ANKRD31	cis	parietal	SCAN
rs246797	ENC1	cis	parietal	SCAN
rs246797	CMYA5	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75642000-75649200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:75646000-75648400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr5:75646000-75649400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:75646200-75648600	Enhancers	Primary B cells from cord blood	blood
5	chr5:75646400-75649200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:75646600-75648000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:75646600-75651000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:75647000-75647800	Enhancers	K562	blood
9	chr5:75647400-75648400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:75647600-75648400	Enhancers	GM12878-XiMat	blood
11	chr5:75647600-75649200	Weak transcription	HUES6 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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