Variant report

Variant	rs7313754
Chromosome Location	chr12:64392500-64392501
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	chr12:64383282..64387924-chr12:64391435..64393983,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM5-3	chr12:64392054-64393594	NONHSAT029126

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10784375	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175217	0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs11175227	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1350138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1350140	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1947504	0.82[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap]
rs3741606	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3741607	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516056	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4604983	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6581515	0.94[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581517	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7300256	0.83[CHB][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs7300468	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];0.98[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9668855	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][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	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
2	nsv747	chr12:64391572-64423998	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
3	nsv437756	chr12:64392500-64411870	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7313754	C12orf66	cis	cerebellum	SCAN
rs7313754	XPOT	cis	cerebellum	SCAN
rs7313754	RPSAP52	cis	parietal	SCAN

Chromatin state (count:56 , 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	chr12:64382800-64399400	Weak transcription	HUVEC	blood vessel
8	chr12:64382800-64432800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:64383000-64401200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:64383600-64393000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:64383600-64397600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:64383800-64425400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:64384600-64404000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:64384800-64394800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:64385000-64401000	Weak transcription	Ovary	ovary
16	chr12:64385000-64408800	Weak transcription	Hela-S3	cervix
17	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
18	chr12:64385200-64399600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:64385800-64399600	Weak transcription	NH-A	brain
20	chr12:64386400-64395200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:64386400-64395600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:64386600-64400000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:64386800-64395200	Weak transcription	Right Atrium	heart
24	chr12:64386800-64397800	Weak transcription	Brain Angular Gyrus	brain
25	chr12:64386800-64403600	Weak transcription	Brain Substantia Nigra	brain
26	chr12:64386800-64404200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:64387400-64396000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:64388800-64392800	Weak transcription	Adipose Nuclei	Adipose
29	chr12:64388800-64393200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:64388800-64394400	Weak transcription	Fetal Brain Female	brain
31	chr12:64388800-64399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:64388800-64399800	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:64388800-64400200	Weak transcription	Fetal Brain Male	brain
34	chr12:64388800-64429800	Weak transcription	Pancreas	Pancrea
35	chr12:64389200-64400000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:64389400-64393000	Weak transcription	Brain Anterior Caudate	brain
37	chr12:64389400-64419200	Weak transcription	Fetal Kidney	kidney
38	chr12:64389400-64419200	Weak transcription	Fetal Lung	lung
39	chr12:64389600-64395600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:64389600-64398200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:64389600-64398200	Weak transcription	Osteobl	bone
42	chr12:64389600-64417400	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:64389800-64392800	Weak transcription	A549	lung
44	chr12:64390000-64393400	Strong transcription	NHDF-Ad	bronchial
45	chr12:64390800-64392600	Strong transcription	HSMM	muscle
46	chr12:64391000-64394000	Strong transcription	NHLF	lung
47	chr12:64391200-64395200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:64391200-64395200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:64391400-64394200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:64391600-64393800	Strong transcription	HSMMtube	muscle

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