Variant report

Variant	rs1541564
Chromosome Location	chr2:40082054-40082055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11692413	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11695763	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12475386	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13424439	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17480505	0.82[ASN][1000 genomes]
rs1861248	0.82[ASN][1000 genomes]
rs2080296	0.83[EUR][1000 genomes]
rs2192703	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2373702	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55768815	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60399093	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62137179	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137180	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137182	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137183	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62137185	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6732387	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556977	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003593	chr2:40009597-40165666	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535651	chr2:40009597-40165666	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv873891	chr2:40046658-40173905	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv430947	chr2:40080723-40141649	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv581496	chr2:40082054-40123904	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1541564	C2orf56	cis	parietal	SCAN
rs1541564	PLEKHH2	cis	cerebellum	SCAN
rs1541564	KCNG3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40077400-40083600	Enhancers	Primary hematopoietic stem cells	blood
2	chr2:40079400-40083000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:40079400-40087600	Weak transcription	HMEC	breast
4	chr2:40079800-40083400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:40081600-40082200	Enhancers	Fetal Thymus	thymus
6	chr2:40081600-40083600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:40081600-40083600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:40081800-40082400	Enhancers	Primary B cells from cord blood	blood
9	chr2:40082000-40082800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:40082000-40082800	Enhancers	Dnd41	blood
11	chr2:40082000-40083400	Enhancers	Thymus	Thymus

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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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