Variant report

Variant	rs7300468
Chromosome Location	chr12:64389491-64389492
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64383466..64385069-chr12:64386859..64389683,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10784375	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175217	0.82[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs11175227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1350138	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1350140	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1947504	0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap]
rs3741606	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741607	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4516056	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4604983	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6581515	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581517	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7300256	0.83[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap]
rs7313754	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957913	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9668855	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7300468	XPOT	cis	cerebellum	SCAN
rs7300468	RPSAP52	cis	parietal	SCAN
rs7300468	C12orf66	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64362800-64396000	Weak transcription	Psoas Muscle	Psoas
2	chr12:64377200-64400200	Weak transcription	Brain Germinal Matrix	brain
3	chr12:64377800-64396400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:64378000-64395200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:64379800-64395200	Weak transcription	Fetal Intestine Small	intestine
6	chr12:64380200-64433000	Weak transcription	Fetal Intestine Large	intestine
7	chr12:64382000-64391200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:64382800-64399400	Weak transcription	HUVEC	blood vessel
9	chr12:64382800-64432800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:64383000-64401200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:64383600-64393000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:64383600-64397600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:64383800-64425400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:64384600-64404000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:64384800-64394800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:64385000-64390800	Weak transcription	HSMM	muscle
17	chr12:64385000-64401000	Weak transcription	Ovary	ovary
18	chr12:64385000-64408800	Weak transcription	Hela-S3	cervix
19	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
20	chr12:64385200-64399600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:64385800-64399600	Weak transcription	NH-A	brain
22	chr12:64386400-64395200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:64386400-64395600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:64386600-64400000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:64386800-64392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:64386800-64392200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:64386800-64395200	Weak transcription	Right Atrium	heart
28	chr12:64386800-64397800	Weak transcription	Brain Angular Gyrus	brain
29	chr12:64386800-64403600	Weak transcription	Brain Substantia Nigra	brain
30	chr12:64386800-64404200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:64387000-64390200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:64387000-64391600	Weak transcription	HSMMtube	muscle
33	chr12:64387400-64396000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:64388000-64389600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:64388600-64389600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:64388600-64389600	Enhancers	Fetal Heart	heart
37	chr12:64388600-64389600	Enhancers	NHDF-Ad	bronchial
38	chr12:64388600-64391800	Enhancers	NHEK	skin
39	chr12:64388800-64389600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:64388800-64390200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:64388800-64392800	Weak transcription	Adipose Nuclei	Adipose
42	chr12:64388800-64393200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:64388800-64394400	Weak transcription	Fetal Brain Female	brain
44	chr12:64388800-64399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:64388800-64399800	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:64388800-64400200	Weak transcription	Fetal Brain Male	brain
47	chr12:64388800-64429800	Weak transcription	Pancreas	Pancrea
48	chr12:64389000-64389600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:64389000-64389600	Enhancers	Osteobl	bone
50	chr12:64389200-64389600	Enhancers	Muscle Satellite Cultured Cells	--

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