Variant report

Variant	rs766505
Chromosome Location	chr12:4875334-4875335
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4873235..4875962-chr12:4887728..4890424,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10431361	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10431362	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10774267	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10849138	0.96[CEU][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10849139	0.96[CEU][hapmap];0.87[YRI][hapmap]
rs11063327	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11063328	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2018895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286581	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2286582	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3782743	0.85[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs4765784	0.93[EUR][1000 genomes]
rs4766284	0.82[JPT][hapmap]
rs7295230	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7295251	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7311675	0.96[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7311694	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7314849	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7315211	0.96[CEU][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs766504	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953399	0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7953482	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7967117	0.96[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7970126	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7973527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7976219	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][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	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1054218	chr12:4819576-4882667	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3332578	chr12:4874835-4877804	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs766505	SLC2A14	cis	parietal	SCAN
rs766505	LOC653113	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4854200-4876000	Weak transcription	Fetal Brain Male	brain
2	chr12:4867200-4880200	Weak transcription	Spleen	Spleen
3	chr12:4869000-4875400	Weak transcription	Fetal Stomach	stomach
4	chr12:4869600-4875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:4869800-4884200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:4871800-4877800	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:4872800-4875600	Weak transcription	Adipose Nuclei	Adipose
8	chr12:4873000-4876400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:4873200-4879800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:4873200-4881800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:4873200-4889800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:4873400-4875600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:4873400-4876200	Weak transcription	Right Atrium	heart
14	chr12:4873400-4876600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:4873400-4881200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:4873400-4889400	Weak transcription	Ovary	ovary
17	chr12:4873600-4876200	Weak transcription	Brain Germinal Matrix	brain
18	chr12:4874400-4875400	Enhancers	Left Ventricle	heart
19	chr12:4874400-4875600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:4874600-4881000	Weak transcription	Fetal Brain Female	brain
21	chr12:4875000-4876200	Weak transcription	Right Ventricle	heart
22	chr12:4875000-4878200	Enhancers	Fetal Muscle Leg	muscle

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