Variant report

Variant	rs12620887
Chromosome Location	chr2:31387929-31387930
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10171858	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10172706	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1443708	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1443709	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1443710	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2044244	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2044245	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2044246	0.83[CEU][hapmap]
rs4952051	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6741329	0.88[CEU][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs961642	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv873771	chr2:31363732-31416582	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv873772	chr2:31363732-31417863	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv873773	chr2:31363732-31426449	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv873774	chr2:31363732-31432367	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873775	chr2:31363732-31439443	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873776	chr2:31384009-31439443	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv997652	chr2:31385242-31431588	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv535611	chr2:31385242-31431588	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12620887	KRTCAP3	cis	cerebellum	SCAN
rs12620887	CLIP4	cis	parietal	SCAN
rs12620887	EIF2B4	cis	cerebellum	SCAN
rs12620887	Hs.468081	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31387800-31388200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:31387800-31388400	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:31387800-31388400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:31387800-31388400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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