Variant report

Variant	rs6581515
Chromosome Location	chr12:64379443-64379444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64311041..64313819-chr12:64377499..64379764,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10784375	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175217	0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs11175227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1350138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1947504	0.82[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2054150	0.84[AFR][1000 genomes]
rs3741606	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741607	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516056	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4604983	0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs6581517	0.97[ASN][1000 genomes]
rs7300256	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]
rs7300468	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]
rs7313754	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]
rs7957913	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9668855	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[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
rs6581515	C12orf66	cis	cerebellum	SCAN
rs6581515	XPOT	cis	cerebellum	SCAN
rs6581515	SRGAP1	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
2	chr12:64362600-64385600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:64362800-64396000	Weak transcription	Psoas Muscle	Psoas
4	chr12:64364200-64385800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:64365000-64383000	Weak transcription	Stomach Mucosa	stomach
6	chr12:64366400-64383600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:64370800-64384400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:64371800-64385800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:64372000-64383200	Weak transcription	Fetal Kidney	kidney
10	chr12:64372400-64382000	Weak transcription	HSMM	muscle
11	chr12:64372800-64380600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:64373800-64383000	Weak transcription	HMEC	breast
13	chr12:64375400-64383200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:64375600-64383200	Weak transcription	Fetal Lung	lung
15	chr12:64375600-64384600	Weak transcription	Hela-S3	cervix
16	chr12:64375800-64385600	Weak transcription	Adipose Nuclei	Adipose
17	chr12:64376200-64385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:64377000-64382000	Weak transcription	Osteobl	bone
19	chr12:64377000-64383200	Weak transcription	Brain Anterior Caudate	brain
20	chr12:64377000-64383400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:64377000-64385400	Weak transcription	Fetal Brain Male	brain
22	chr12:64377200-64381000	Strong transcription	A549	lung
23	chr12:64377200-64382000	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:64377200-64382000	Weak transcription	Brain Substantia Nigra	brain
25	chr12:64377200-64382200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:64377200-64382200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:64377200-64383000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:64377200-64383000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:64377200-64383200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:64377200-64383200	Weak transcription	HSMMtube	muscle
31	chr12:64377200-64383400	Weak transcription	Brain Angular Gyrus	brain
32	chr12:64377200-64383400	Weak transcription	NH-A	brain
33	chr12:64377200-64400200	Weak transcription	Brain Germinal Matrix	brain
34	chr12:64377400-64382400	Weak transcription	Fetal Stomach	stomach
35	chr12:64377400-64382600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:64377600-64380000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:64377800-64379600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:64377800-64381600	Strong transcription	NHDF-Ad	bronchial
39	chr12:64377800-64382000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:64377800-64396400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:64378000-64383200	Weak transcription	HepG2	liver
42	chr12:64378000-64395200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:64378200-64381800	Weak transcription	NHEK	skin
44	chr12:64378600-64379800	Strong transcription	Fetal Intestine Small	intestine
45	chr12:64378800-64379600	Strong transcription	Fetal Brain Female	brain
46	chr12:64378800-64379800	Genic enhancers	Esophagus	oesophagus
47	chr12:64378800-64379800	Genic enhancers	Pancreas	Pancrea
48	chr12:64378800-64380000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:64378800-64380000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:64378800-64380600	Strong transcription	NHLF	lung

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