Variant report

Variant	rs628408
Chromosome Location	chr12:45067278-45067279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1037433	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1037434	0.88[ASN][1000 genomes]
rs10506256	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10748400	0.87[ASN][1000 genomes]
rs10785515	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10880657	0.86[ASN][1000 genomes]
rs10880658	0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs10880659	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10880660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880666	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[MKK][hapmap];0.85[ASN][1000 genomes]
rs10880673	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11182559	0.84[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11182596	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11182599	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11182634	0.85[ASN][1000 genomes]
rs11182635	0.85[ASN][1000 genomes]
rs11182636	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11182640	0.85[ASN][1000 genomes]
rs12303497	0.82[ASN][1000 genomes]
rs12312100	0.84[ASN][1000 genomes]
rs12812414	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12815257	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs1563043	0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1850406	1.00[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1869162	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs2084843	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2305448	0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3858727	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4544065	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs4768066	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4768563	0.86[ASN][1000 genomes]
rs4768564	0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs581473	0.85[ASN][1000 genomes]
rs583575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605722	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs615760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs678663	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs688669	0.91[ASN][1000 genomes]
rs7295999	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7299365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301539	1.00[CEU][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7302107	0.90[EUR][1000 genomes]
rs7308509	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7310844	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7314643	0.92[ASN][1000 genomes]
rs7958389	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7968076	0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7970849	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs838973	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs966383	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs978540	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv430506	chr12:45003342-45072343	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs628408	SLC38A1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45049400-45069000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:45051800-45081200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:45056600-45083800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:45062400-45081200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:45064200-45068600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:45064600-45067600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:45065000-45116000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:45066600-45069000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:45066800-45068000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:45066800-45083000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr12:45067200-45072400	Enhancers	Fetal Brain Male	brain

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