Variant report

Variant	rs12308338
Chromosome Location	chr12:68569191-68569192
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11177072	0.84[EUR][1000 genomes]
rs11177073	0.83[EUR][1000 genomes]
rs11177074	0.83[ASN][1000 genomes]
rs11503734	0.83[EUR][1000 genomes]
rs11831576	1.00[ASN][1000 genomes]
rs11835593	0.90[ASN][1000 genomes]
rs12306852	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307587	0.83[EUR][1000 genomes]
rs12310687	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313843	0.90[EUR][1000 genomes]
rs12318069	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320174	0.89[EUR][1000 genomes]
rs12321504	0.88[EUR][1000 genomes]
rs12321565	0.84[EUR][1000 genomes]
rs2069728	0.83[ASN][1000 genomes]
rs2193035	0.90[ASN][1000 genomes]
rs3181032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3181035	0.83[ASN][1000 genomes]
rs55881326	0.84[EUR][1000 genomes]
rs56408274	0.90[EUR][1000 genomes]
rs57680423	1.00[ASN][1000 genomes]
rs60017528	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60079212	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923089	0.83[EUR][1000 genomes]
rs61923118	0.89[EUR][1000 genomes]
rs61923119	0.89[EUR][1000 genomes]
rs61923151	0.89[EUR][1000 genomes]
rs7296336	0.83[ASN][1000 genomes]
rs7296352	0.83[ASN][1000 genomes]
rs7956688	0.90[ASN][1000 genomes]
rs7959900	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1847952	chr12:68544896-68693242	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12308338	RASSF3	cis	cerebellum	SCAN
rs12308338	SRGAP1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68557200-68569600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:68567200-68569200	Enhancers	Primary T cells from cord blood	blood
3	chr12:68567400-68569200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr12:68568400-68569200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:68568400-68569400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:68568600-68569200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:68568800-68569200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:68568800-68569200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:68568800-68569400	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:68568800-68569400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:68568800-68570400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr12:68568800-68570400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr12:68568800-68572000	Enhancers	Fetal Thymus	thymus
14	chr12:68569000-68569200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr12:68569000-68569200	Enhancers	GM12878-XiMat	blood
16	chr12:68569000-68569400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr12:68569000-68570000	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr12:68569000-68570200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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