Variant report

Variant	rs4083381
Chromosome Location	chr3:60037145-60037146
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs182418	0.87[MEX][hapmap]
rs212003	0.85[CHB][hapmap]
rs212043	0.87[MEX][hapmap]
rs212045	0.81[CHB][hapmap]
rs212059	0.92[MEX][hapmap]
rs35138137	0.88[ASN][1000 genomes]
rs3845972	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3912495	0.90[CEU][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6801817	0.83[CHB][hapmap]
rs73092171	0.82[ASN][1000 genomes]
rs9311746	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][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	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	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
3	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
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS 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	1 gene(s)	inside rSNPs	diseases
5	nsv876839	chr3:60024084-60039488	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4083381	SPATA12	cis	parietal	SCAN
rs4083381	SYNPR	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60034600-60044400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr3:60034800-60037600	Enhancers	Dnd41	blood
3	chr3:60034800-60038000	Weak transcription	Thymus	Thymus
4	chr3:60034800-60041400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:60035000-60038200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:60035000-60038200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:60035000-60039000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr3:60035000-60041200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:60035000-60043200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:60035000-60043200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:60035200-60038200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:60035400-60041400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:60036200-60037200	Enhancers	Fetal Thymus	thymus
14	chr3:60036400-60037200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:60036600-60038000	Weak transcription	Primary T cells from cord blood	blood
16	chr3:60036800-60041200	Enhancers	Primary T helper naive cells 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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