Variant report

Variant	rs7300256
Chromosome Location	chr12:64366408-64366409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64362929..64364483-chr12:64366309..64367856,2	MCF-7	breast:
2	chr12:64366069..64368652-chr12:64370868..64372528,3	MCF-7	breast:
3	chr12:64361242..64364159-chr12:64364503..64367184,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11175217	0.86[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175227	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1350138	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1350140	0.85[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs1947504	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1962538	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2054150	0.92[ASN][1000 genomes]
rs3741606	0.81[EUR][1000 genomes]
rs3741607	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs4516056	0.94[JPT][hapmap]
rs4604983	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6581515	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs6581517	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7300468	0.83[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap]
rs7313754	0.83[CHB][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs7957913	0.83[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs9668855	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][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	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	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
3	nsv559201	chr12:64333212-64366408	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7300256	XPOT	cis	cerebellum	SCAN
rs7300256	C12orf66	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
2	chr12:64361800-64371600	Weak transcription	HMEC	breast
3	chr12:64361800-64371800	Weak transcription	NH-A	brain
4	chr12:64362000-64367600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:64362000-64369800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:64362000-64371600	Weak transcription	NHEK	skin
7	chr12:64362400-64367600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:64362600-64371600	Weak transcription	HSMM	muscle
9	chr12:64362600-64371800	Weak transcription	Brain Substantia Nigra	brain
10	chr12:64362600-64371800	Weak transcription	Osteobl	bone
11	chr12:64362600-64385600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:64362800-64366800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:64362800-64367000	Weak transcription	NHDF-Ad	bronchial
14	chr12:64362800-64377600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:64362800-64378800	Weak transcription	Pancreas	Pancrea
16	chr12:64362800-64396000	Weak transcription	Psoas Muscle	Psoas
17	chr12:64363000-64371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:64363200-64367600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:64364000-64370000	Weak transcription	NHLF	lung
20	chr12:64364200-64366600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:64364200-64367000	Weak transcription	Ovary	ovary
22	chr12:64364200-64367600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:64364200-64376200	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:64364200-64376800	Weak transcription	HSMMtube	muscle
25	chr12:64364200-64385800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:64365000-64366800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:64365000-64367000	Weak transcription	A549	lung
28	chr12:64365000-64371400	Weak transcription	Fetal Kidney	kidney
29	chr12:64365000-64375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:64365000-64383000	Weak transcription	Stomach Mucosa	stomach
31	chr12:64365800-64378600	Weak transcription	Fetal Intestine Small	intestine
32	chr12:64365800-64379400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:64366400-64383600	Weak transcription	Rectal Mucosa Donor 31	rectum

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