Variant report

Variant	rs13070338
Chromosome Location	chr3:60064296-60064297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11718208	0.92[CHB][hapmap]
rs11718957	0.92[CHB][hapmap]
rs11927585	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13058814	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13066837	0.92[CHB][hapmap]
rs13069706	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075738	0.92[CHB][hapmap]
rs17322850	0.92[CHB][hapmap]
rs17325451	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2361335	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2736781	0.85[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2736782	0.85[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2736787	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736789	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3843360	0.92[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs3856670	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv523496	chr3:60059041-60064296	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv519729	chr3:60062654-60064296	Weak transcription Flanking Active TSS Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13070338	SYNPR	cis	cerebellum	SCAN
rs13070338	FAM116A	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60059800-60064800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:60061800-60066400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:60061800-60068400	Flanking Active TSS	Dnd41	blood
4	chr3:60062400-60064600	Weak transcription	Thymus	Thymus
5	chr3:60062400-60065200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:60062400-60066200	Weak transcription	Stomach Mucosa	stomach
7	chr3:60062400-60066400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:60062400-60066400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:60062800-60064800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:60063000-60066000	Weak transcription	Primary B cells from cord blood	blood
11	chr3:60063400-60066600	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr3:60063600-60065000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:60063600-60066000	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:60063600-60066800	Active TSS	Primary T cells fromperipheralblood	blood
15	chr3:60063800-60066400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr3:60063800-60068000	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr3:60064000-60064400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr3:60064000-60064400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:60064200-60064400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:60064200-60064600	Active TSS	Fetal Thymus	thymus
21	chr3:60064200-60066200	Active TSS	Primary T killer memory cells from peripheral blood	blood

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