Variant report

Variant	rs12248932
Chromosome Location	chr10:93643485-93643486
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93642306..93644379-chr10:93658449..93661429,2	MCF-7	breast:
2	chr10:93638890..93643512-chr10:93665882..93670219,9	MCF-7	breast:
3	chr10:93643244..93645164-chr10:93648326..93650268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174721	Chromatin interaction
ENSG00000272817	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10736064	0.83[EUR][1000 genomes]
rs10748568	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10748569	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10786011	0.81[EUR][1000 genomes]
rs10786013	0.82[EUR][1000 genomes]
rs10786015	0.83[EUR][1000 genomes]
rs10786018	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10881959	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs10881968	0.87[EUR][1000 genomes]
rs11186695	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11186726	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11186731	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11814405	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1340420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1539041	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1572933	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1572934	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1770467	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1770470	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1770472	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1770475	0.85[EUR][1000 genomes]
rs1772180	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1772185	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1935030	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1935031	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2066276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2259280	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487513	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2487514	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2994394	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403720	0.83[EUR][1000 genomes]
rs6583787	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66627345	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7079825	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7085519	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897784	0.82[EUR][1000 genomes]
rs7911346	0.88[EUR][1000 genomes]
rs946896	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv7491	chr10:93626192-93671694	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1842657	chr10:93634155-93668663	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12248932	TNKS2-AS1	cis	Thyroid	GTEx
rs12248932	TNKS2-AS1	cis	Esophagus Muscularis	GTEx
rs12248932	TNKS2-AS1	cis	Muscle Skeletal	GTEx
rs12248932	TNKS2-AS1	cis	Artery Tibial	GTEx
rs12248932	TNKS2-AS1	cis	Stomach	GTEx
rs12248932	TNKS2-AS1	cis	Nerve Tibial	GTEx
rs12248932	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs12248932	TNKS2-AS1	cis	lung	GTEx
rs12248932	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx
rs12248932	TNKS2-AS1	cis	Artery Aorta	GTEx
rs12248932	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs12248932	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93640600-93644800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:93642600-93645000	Enhancers	Placenta	Placenta
3	chr10:93643000-93643600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:93643000-93644200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr10:93643000-93644200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:93643000-93644200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:93643000-93644200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr10:93643000-93644600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr10:93643000-93645600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:93643000-93645800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:93643000-93645800	Enhancers	Fetal Brain Male	brain
12	chr10:93643200-93643600	Active TSS	Brain Anterior Caudate	brain
13	chr10:93643200-93643600	Active TSS	Brain Hippocampus Middle	brain
14	chr10:93643200-93643600	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr10:93643200-93643600	Enhancers	Esophagus	oesophagus
16	chr10:93643200-93643600	Flanking Active TSS	Psoas Muscle	Psoas
17	chr10:93643200-93643600	Flanking Active TSS	Right Atrium	heart
18	chr10:93643200-93643800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr10:93643200-93643800	Active TSS	Aorta	Aorta
20	chr10:93643200-93643800	Enhancers	Brain Angular Gyrus	brain
21	chr10:93643200-93643800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
22	chr10:93643200-93643800	Flanking Active TSS	Fetal Kidney	kidney
23	chr10:93643200-93643800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr10:93643200-93643800	Enhancers	Lung	lung
25	chr10:93643200-93643800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr10:93643200-93643800	Enhancers	Stomach Mucosa	stomach
27	chr10:93643200-93643800	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr10:93643200-93643800	Enhancers	HSMM	muscle
29	chr10:93643200-93643800	Flanking Active TSS	HSMMtube	muscle
30	chr10:93643200-93644000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr10:93643200-93644000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:93643200-93644000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:93643200-93644000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:93643200-93644000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr10:93643200-93644000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr10:93643200-93644000	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr10:93643200-93644000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr10:93643200-93644000	Flanking Active TSS	NH-A	brain
39	chr10:93643200-93644000	Flanking Active TSS	NHEK	skin
40	chr10:93643200-93644000	Flanking Active TSS	Osteobl	bone
41	chr10:93643200-93644200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr10:93643200-93644200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr10:93643200-93644200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr10:93643200-93644200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr10:93643200-93644200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr10:93643200-93644200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr10:93643200-93644200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr10:93643200-93644400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr10:93643200-93644400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:93643200-93644400	Enhancers	Colon Smooth Muscle	Colon

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