Variant report

Variant	rs2329401
Chromosome Location	chr7:39553810-39553811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11772773	0.84[AMR][1000 genomes]
rs17687693	0.83[ASN][1000 genomes]
rs2329402	0.83[ASN][1000 genomes]
rs2329405	0.81[ASN][1000 genomes]
rs2329406	0.82[AMR][1000 genomes]
rs2329407	0.81[ASN][1000 genomes]
rs2329408	0.81[ASN][1000 genomes]
rs4599720	0.99[ASN][1000 genomes]
rs4720325	0.83[ASN][1000 genomes]
rs4723874	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4723875	0.82[ASN][1000 genomes]
rs6967653	0.82[ASN][1000 genomes]
rs734460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784744	0.83[ASN][1000 genomes]
rs9639813	0.82[ASN][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	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv966782	chr7:39454992-39581886	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv1792839	chr7:39547573-39554212	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	esv1838867	chr7:39547573-39554212	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv1838963	chr7:39547573-39554212	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv1839801	chr7:39547573-39554212	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv606690	chr7:39547573-39554212	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2329401	VPS41	cis	parietal	SCAN
rs2329401	AMPH	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39551600-39555000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr7:39551800-39556400	Weak transcription	Dnd41	blood
3	chr7:39553600-39555800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:39553600-39556000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:39553800-39554200	Weak transcription	Primary hematopoietic stem cells	blood

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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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