Variant report

Variant	rs1908179
Chromosome Location	chr12:44934496-44934497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1037435	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1037436	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs10785501	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10785505	0.95[JPT][hapmap]
rs10785506	0.95[JPT][hapmap]
rs10785507	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10785509	0.90[JPT][hapmap]
rs10785511	0.90[JPT][hapmap]
rs10880649	0.96[ASN][1000 genomes]
rs10880650	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10880651	0.98[ASN][1000 genomes]
rs10880653	0.90[JPT][hapmap]
rs10880654	0.90[JPT][hapmap]
rs11182530	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182531	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231246	0.81[JPT][hapmap]
rs12815663	0.81[JPT][hapmap]
rs1349621	0.95[JPT][hapmap]
rs1376997	0.95[JPT][hapmap]
rs1377003	0.86[JPT][hapmap]
rs1377280	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1452256	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1452257	0.95[JPT][hapmap]
rs1493748	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1552860	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1869253	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs1901556	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2198338	0.93[ASN][1000 genomes]
rs2218986	0.91[ASN][1000 genomes]
rs2270479	0.81[JPT][hapmap]
rs2859835	0.99[ASN][1000 genomes]
rs4143007	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs4768555	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4768556	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4768560	0.81[JPT][hapmap]
rs61930799	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728065	0.95[JPT][hapmap]
rs7953009	0.96[ASN][1000 genomes]
rs7953156	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7966066	0.85[CHD][hapmap];0.95[JPT][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1908179	SLC38A1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44904600-44936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:44909200-44939800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:44918600-44972000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:44924400-44939800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:44924800-44939800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:44925600-44936200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:44926400-44936600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:44932400-44937200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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