Variant report

Variant	rs1850406
Chromosome Location	chr12:45045537-45045538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1037433	0.81[ASN][1000 genomes]
rs10506256	0.88[CHD][hapmap];0.81[GIH][hapmap]
rs10785515	0.83[ASN][1000 genomes]
rs10880660	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10880666	0.81[CHD][hapmap]
rs11182596	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11182599	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11182636	0.81[CHD][hapmap]
rs12812414	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815257	0.81[ASN][1000 genomes]
rs1563043	0.80[ASN][1000 genomes]
rs2084843	0.80[ASN][1000 genomes]
rs2305448	0.88[CHD][hapmap];0.89[GIH][hapmap]
rs3858727	0.88[EUR][1000 genomes]
rs4544065	0.87[CHD][hapmap];0.91[GIH][hapmap]
rs4768564	0.90[CHD][hapmap];0.91[GIH][hapmap]
rs583575	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs615760	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs628408	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]
rs632481	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs636843	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7295999	0.81[ASN][1000 genomes]
rs7299365	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7301539	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302107	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7310844	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7314643	0.81[ASN][1000 genomes]
rs7968076	0.83[ASN][1000 genomes]
rs966383	0.83[ASN][1000 genomes]
rs978540	0.83[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	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
4	esv2762978	chr12:45042460-45051490	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1850406	SLC38A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45015000-45048400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:45023400-45055600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:45031600-45059200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:45036600-45046600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45042400-45047600	Weak transcription	Fetal Brain Female	brain
6	chr12:45042400-45047800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:45042400-45047800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:45043400-45047200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:45043600-45047400	Weak transcription	Fetal Brain Male	brain
10	chr12:45043600-45047800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:45043600-45048400	Weak transcription	Fetal Stomach	stomach
12	chr12:45043800-45047800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:45043800-45048000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:45043800-45048200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:45043800-45048200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:45043800-45048400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:45043800-45054000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:45044000-45047600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:45044400-45062800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:45045000-45048400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:45045200-45047800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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