Variant report

Variant	rs2366968
Chromosome Location	chr3:59916314-59916315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1038516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10510820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12489929	1.00[CHB][hapmap]
rs12490525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17253376	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17309998	1.00[CHB][hapmap]
rs17374239	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17375293	1.00[CHB][hapmap]
rs212040	1.00[CHB][hapmap]
rs3772446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3772466	1.00[CHB][hapmap]
rs3772479	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6783428	0.86[EUR][1000 genomes]
rs6786862	1.00[CHB][hapmap]
rs931317	1.00[CHB][hapmap]
rs931320	0.80[EUR][1000 genomes]
rs931321	1.00[CHB][hapmap]
rs9877140	1.00[CHB][hapmap]

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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2366968	SPATA12	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59905000-59917800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:59905600-59918600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:59914200-59920800	Weak transcription	Dnd41	blood
4	chr3:59914800-59919800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:59914800-59928400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:59915600-59918800	Enhancers	Fetal Thymus	thymus
7	chr3:59915600-59922600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr3:59915800-59916400	Enhancers	Thymus	Thymus
9	chr3:59915800-59917800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr3:59915800-59919400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:59915800-59925400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:59916000-59917200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr3:59916000-59917800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:59916200-59916400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:59916200-59921400	Enhancers	Primary T cells from cord blood	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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