Variant report

Variant	rs3110950
Chromosome Location	chr12:10116615-10116616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11053533	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11053536	0.90[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap]
rs11053538	0.92[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs11053548	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs2273987	0.92[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2922163	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2961540	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2961541	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818343	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs471521	0.80[EUR][1000 genomes]
rs556300	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs611819	0.92[JPT][hapmap]
rs648985	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652944	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs673173	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs676397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044587	chr12:10029514-10123414	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv523050	chr12:10031880-10124373	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3110950	C1S	cis	parietal	SCAN
rs3110950	CLEC4C	cis	cerebellum	SCAN
rs3110950	NCAPD2	cis	parietal	SCAN
rs3110950	GPR19	cis	parietal	SCAN
rs3110950	ING4	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10114600-10117000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:10115400-10117200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:10116600-10117000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr12:10116600-10117800	Enhancers	Primary neutrophils fromperipheralblood	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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