Variant report

Variant	rs9311746
Chromosome Location	chr3:60040012-60040013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11711227	0.92[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11718994	0.88[EUR][1000 genomes]
rs13062399	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs13081934	0.85[CEU][hapmap]
rs13088111	0.92[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs212003	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs212045	0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs34476175	0.90[EUR][1000 genomes]
rs35138137	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3843360	0.82[MEX][hapmap]
rs3845972	0.89[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs3845974	0.83[ASW][hapmap]
rs4083381	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs62238444	0.84[EUR][1000 genomes]
rs6801817	0.83[CHB][hapmap]
rs73092171	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9311746	SYNPR	cis	cerebellum	SCAN

Chromatin state (count:20 , 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	chr3:60034800-60041400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:60035000-60041200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:60035000-60043200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:60035000-60043200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr3:60035400-60041400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:60036800-60041200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:60037200-60040800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:60038000-60042800	Enhancers	Thymus	Thymus
10	chr3:60038200-60042800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr3:60038200-60043600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:60038600-60043000	Enhancers	Primary T cells from cord blood	blood
13	chr3:60038800-60041000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:60039400-60041200	Weak transcription	NH-A	brain
15	chr3:60039400-60043200	Enhancers	Fetal Thymus	thymus
16	chr3:60039600-60040200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr3:60039600-60041400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:60039600-60041400	Weak transcription	NHEK	skin
19	chr3:60039600-60041600	Enhancers	Dnd41	blood
20	chr3:60039800-60041600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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