Variant report

Variant	rs1350140
Chromosome Location	chr12:64387329-64387330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64383282..64387924-chr12:64391435..64393983,4	MCF-7	breast:
2	chr12:64383466..64385069-chr12:64386859..64389683,2	MCF-7	breast:
3	chr12:64385805..64388155-chr3:161131123..161133119,2	MCF-7	breast:
4	chr12:64386194..64388353-chr12:64398792..64400563,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10784375	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175217	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs11175227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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];0.99[ASN][1000 genomes]
rs1947504	0.82[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[TSI][hapmap]
rs3741606	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741607	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516056	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4604983	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6581515	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]
rs6581517	0.97[ASN][1000 genomes]
rs7300256	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]
rs7300468	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]
rs7313754	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]
rs7957913	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9668855	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1350140	C12orf66	cis	cerebellum	SCAN
rs1350140	XPOT	cis	cerebellum	SCAN

Chromatin state (count:64 , 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	chr12:64379800-64388400	Weak transcription	Fetal Brain Female	brain
6	chr12:64379800-64395200	Weak transcription	Fetal Intestine Small	intestine
7	chr12:64380200-64433000	Weak transcription	Fetal Intestine Large	intestine
8	chr12:64382000-64391200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:64382800-64399400	Weak transcription	HUVEC	blood vessel
10	chr12:64382800-64432800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:64383000-64401200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:64383600-64393000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:64383600-64397600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:64383800-64388200	Weak transcription	Stomach Mucosa	stomach
15	chr12:64383800-64425400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:64384000-64387400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:64384600-64387400	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr12:64384600-64404000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:64384800-64388200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:64384800-64394800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:64385000-64390800	Weak transcription	HSMM	muscle
22	chr12:64385000-64401000	Weak transcription	Ovary	ovary
23	chr12:64385000-64408800	Weak transcription	Hela-S3	cervix
24	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
25	chr12:64385200-64399600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:64385600-64389000	Weak transcription	Osteobl	bone
27	chr12:64385800-64399600	Weak transcription	NH-A	brain
28	chr12:64386000-64387600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:64386000-64388200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:64386000-64388200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:64386000-64388400	Weak transcription	Fetal Brain Male	brain
32	chr12:64386000-64388400	Weak transcription	Fetal Kidney	kidney
33	chr12:64386200-64387800	Enhancers	Fetal Heart	heart
34	chr12:64386400-64387400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:64386400-64388200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:64386400-64388400	Weak transcription	Pancreas	Pancrea
37	chr12:64386400-64395200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:64386400-64395600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:64386600-64389200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:64386600-64400000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:64386800-64388200	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:64386800-64388200	Weak transcription	Fetal Lung	lung
43	chr12:64386800-64388200	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:64386800-64388200	Weak transcription	Fetal Stomach	stomach
45	chr12:64386800-64388200	Enhancers	NHDF-Ad	bronchial
46	chr12:64386800-64388600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:64386800-64388600	Weak transcription	Brain Anterior Caudate	brain
48	chr12:64386800-64388600	Weak transcription	NHEK	skin
49	chr12:64386800-64389000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:64386800-64392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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