Variant report

Variant	rs1340420
Chromosome Location	chr10:93617306-93617307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93615667..93617666-chr10:93667946..93669465,10	MCF-7	breast:
2	chr10:93612504..93620868-chr10:93666635..93670170,8	MCF-7	breast:
3	chr10:93614162..93618844-chr10:93665792..93669898,8	MCF-7	breast:
4	chr10:93617118..93618741-chr10:93621503..93623956,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272817	Chromatin interaction
ENSG00000174721	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10736064	0.88[EUR][1000 genomes]
rs10736065	0.83[EUR][1000 genomes]
rs10748568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10748569	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786011	0.86[EUR][1000 genomes]
rs10786013	0.87[EUR][1000 genomes]
rs10786015	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10881959	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs10881968	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11186695	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11186726	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11186731	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11814405	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12248932	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[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1572933	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1572934	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1770467	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770475	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1772180	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772185	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1935031	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2066276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2259280	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2487513	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2487514	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2994394	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3930831	0.84[EUR][1000 genomes]
rs4403720	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6583787	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66627345	0.93[ASN][1000 genomes]
rs7073486	0.83[EUR][1000 genomes]
rs7077236	0.84[EUR][1000 genomes]
rs7079825	0.80[EUR][1000 genomes]
rs7085519	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7897784	0.87[EUR][1000 genomes]
rs7911346	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7918126	0.84[EUR][1000 genomes]
rs946896	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1340420	TNKS2-AS1	cis	Thyroid	GTEx
rs1340420	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs1340420	TNKS2-AS1	cis	Nerve Tibial	GTEx
rs1340420	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs1340420	PPP1R3C	cis	Esophagus Mucosa	GTEx
rs1340420	TNKS2-AS1	cis	Artery Aorta	GTEx
rs1340420	TNKS2-AS1	cis	Artery Tibial	GTEx
rs1340420	TNKS2-AS1	cis	lung	GTEx
rs1340420	TNKS2-AS1	cis	Muscle Skeletal	GTEx
rs1340420	TNKS2-AS1	cis	Esophagus Muscularis	GTEx
rs1340420	TNKS2-AS1	cis	Stomach	GTEx
rs1340420	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1340420	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93567200-93624200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr10:93569200-93626800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:93570800-93625000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr10:93570800-93626000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:93570800-93626000	Strong transcription	Dnd41	blood
6	chr10:93571000-93623200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr10:93571000-93624000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr10:93571000-93625800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr10:93571200-93626400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:93571400-93626400	Strong transcription	Liver	Liver
11	chr10:93571400-93626400	Strong transcription	Fetal Thymus	thymus
12	chr10:93572000-93626200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr10:93572000-93626400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr10:93572000-93626400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:93572200-93623600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr10:93572200-93625600	Strong transcription	Placenta	Placenta
17	chr10:93572200-93626400	Strong transcription	Primary B cells from cord blood	blood
18	chr10:93572400-93623000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr10:93572400-93624400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr10:93572400-93624800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr10:93572400-93626000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr10:93572400-93626000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr10:93572400-93626000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:93572400-93626200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:93572400-93626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:93572600-93624400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:93572600-93626200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr10:93572600-93626200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr10:93572600-93626200	Strong transcription	Adipose Nuclei	Adipose
30	chr10:93572600-93626600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:93572600-93629000	Weak transcription	Stomach Mucosa	stomach
32	chr10:93572800-93626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:93573000-93626200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:93573400-93624400	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr10:93576600-93624400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr10:93577000-93624800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:93580000-93624600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr10:93584200-93626400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr10:93585400-93626200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr10:93586200-93624200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:93591800-93626200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr10:93593400-93624200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:93593800-93623000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr10:93594200-93622600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:93598400-93629000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr10:93599200-93629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr10:93599600-93634600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:93601800-93620600	Strong transcription	HepG2	liver
49	chr10:93605600-93625600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr10:93606400-93625400	Weak transcription	Spleen	Spleen

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