Variant report

Variant	rs7972782
Chromosome Location	chr12:10402829-10402830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10505759	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10845081	0.82[CHB][hapmap]
rs10845099	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11053725	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs1600130	0.81[TSI][hapmap]
rs3912117	0.81[TSI][hapmap]
rs4254156	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs4764331	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs4764341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7314888	0.80[TSI][hapmap]
rs765791	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7961687	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs7975352	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7976020	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]

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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7972782	NOP2	cis	cerebellum	SCAN
rs7972782	GRIN2B	cis	cerebellum	SCAN
rs7972782	CLEC4A	cis	cerebellum	SCAN
rs7972782	APOLD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10377800-10404400	Weak transcription	Left Ventricle	heart
2	chr12:10397200-10403000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:10398800-10436200	Weak transcription	Placenta	Placenta
4	chr12:10399400-10405200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:10401600-10403800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:10402000-10403200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:10402200-10403000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:10402400-10403000	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:10402400-10403200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr12:10402400-10403200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:10402400-10403200	Enhancers	Dnd41	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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