Variant report

Variant	rs12316767
Chromosome Location	chr12:47170621-47170622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47170591..47173470-chr12:47179230..47182105,2	MCF-7	breast:
2	chr12:46885590..46888355-chr12:47169213..47171245,2	MCF-7	breast:
3	chr12:47168903..47170642-chr12:47170948..47173007,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11183581	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11183589	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183605	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183608	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615446	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12303637	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12307895	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12311710	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12313822	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12318216	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12320235	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12320632	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12322157	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12582305	0.82[JPT][hapmap]
rs180403	0.87[CEU][hapmap]
rs180405	0.87[CEU][hapmap]
rs180408	0.87[CEU][hapmap]
rs180410	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs180412	0.85[EUR][1000 genomes]
rs180415	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs180416	0.94[EUR][1000 genomes]
rs180417	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs180419	0.88[EUR][1000 genomes]
rs180420	0.82[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs180421	0.87[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs180426	0.93[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs180429	0.85[GIH][hapmap]
rs180430	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[EUR][1000 genomes]
rs2111773	0.88[AMR][1000 genomes]
rs2287471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408621	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2465582	0.87[CEU][hapmap]
rs2465584	0.87[CEU][hapmap]
rs4768136	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768751	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56819961	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12316767	SLC38A4	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47157400-47172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:47161600-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:47164200-47187800	Genic enhancers	Liver	Liver
4	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
5	chr12:47165600-47182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:47167000-47173200	Enhancers	HepG2	liver
7	chr12:47168400-47177600	Weak transcription	NHLF	lung
8	chr12:47168400-47180800	Weak transcription	Pancreas	Pancrea
9	chr12:47169000-47173600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:47169000-47177600	Weak transcription	HSMMtube	muscle
11	chr12:47169200-47171800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:47169200-47175600	Strong transcription	HSMM	muscle
13	chr12:47169400-47172000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:47169400-47180000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:47169400-47182200	Weak transcription	Psoas Muscle	Psoas
16	chr12:47169400-47185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:47169600-47171000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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