Variant report

Variant	rs3181030
Chromosome Location	chr1:158220291-158220292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1042388	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12738822	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12738901	0.87[AMR][1000 genomes]
rs12745422	0.87[AMR][1000 genomes]
rs12751724	0.91[AMR][1000 genomes]
rs34015891	0.87[AMR][1000 genomes]
rs34059172	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34120202	0.87[AMR][1000 genomes]
rs34250639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34431925	0.87[AMR][1000 genomes]
rs34811385	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34835673	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35136907	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35554638	0.87[AMR][1000 genomes]
rs35669445	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7527282	0.83[AMR][1000 genomes]
rs959518	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]

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	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv508626	chr1:158161932-158242158	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1845799	chr1:158175976-158230829	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3181030	CD1A	cis	multi-tissue	Pritchard
rs3181030	C1orf68	cis	cerebellum	SCAN
rs3181030	LMNA	cis	parietal	SCAN
rs3181030	S100A2	cis	parietal	SCAN
rs3181030	ATP1A4	cis	cerebellum	SCAN
rs3181030	TMEM79	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158216400-158222400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:158216600-158221200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:158217000-158220600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:158217400-158220600	Flanking Active TSS	Dnd41	blood
5	chr1:158218800-158221600	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:158219000-158221600	Enhancers	Primary B cells from cord blood	blood
7	chr1:158219200-158223800	Enhancers	Fetal Thymus	thymus
8	chr1:158220000-158222000	Enhancers	Thymus	Thymus

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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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