Variant report

Variant	rs1539042
Chromosome Location	chr10:93624017-93624018
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	chr10:93622435..93625235-chr10:93666219..93668406,2	MCF-7	breast:
2	chr10:93623670..93626355-chr10:93627411..93630158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272817	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10509634	0.82[JPT][hapmap]
rs10881966	0.82[JPT][hapmap]
rs10881967	0.85[JPT][hapmap]
rs10881973	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10881974	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10881978	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10881979	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10881987	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10881988	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186696	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11186719	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11186721	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11186722	0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186723	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11598220	0.85[JPT][hapmap]
rs12253245	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1592050	0.85[JPT][hapmap]
rs1770466	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1770476	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1772179	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1772182	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1772183	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1772189	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890896	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153655	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2259305	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275646	0.84[JPT][hapmap]
rs2421698	0.84[JPT][hapmap]
rs2994393	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802650	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4611111	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4612711	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4933698	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7069232	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7072165	0.84[JPT][hapmap]
rs7076618	0.84[JPT][hapmap]
rs7076687	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7079479	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7096581	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7895548	0.85[JPT][hapmap]
rs7901710	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7917858	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1539042	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs1539042	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs1539042	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx
rs1539042	TNKS2-AS1	cis	Artery Tibial	GTEx
rs1539042	TNKS2-AS1	cis	lung	GTEx
rs1539042	TNKS2-AS1	cis	Thyroid	GTEx
rs1539042	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1539042	TNKS2-AS1	cis	Muscle Skeletal	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	chr10:93571000-93625800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr10:93571200-93626400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:93571400-93626400	Strong transcription	Liver	Liver
9	chr10:93571400-93626400	Strong transcription	Fetal Thymus	thymus
10	chr10:93572000-93626200	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr10:93572000-93626400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr10:93572000-93626400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr10:93572200-93625600	Strong transcription	Placenta	Placenta
14	chr10:93572200-93626400	Strong transcription	Primary B cells from cord blood	blood
15	chr10:93572400-93624400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr10:93572400-93624800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr10:93572400-93626000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:93572400-93626000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr10:93572400-93626000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:93572400-93626200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:93572400-93626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:93572600-93624400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:93572600-93626200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr10:93572600-93626200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr10:93572600-93626200	Strong transcription	Adipose Nuclei	Adipose
26	chr10:93572600-93626600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:93572600-93629000	Weak transcription	Stomach Mucosa	stomach
28	chr10:93572800-93626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:93573000-93626200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:93573400-93624400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr10:93576600-93624400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:93577000-93624800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:93580000-93624600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:93584200-93626400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr10:93585400-93626200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:93586200-93624200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:93591800-93626200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr10:93593400-93624200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr10:93598400-93629000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr10:93599200-93629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr10:93599600-93634600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:93605600-93625600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr10:93606400-93625400	Weak transcription	Spleen	Spleen
44	chr10:93606400-93630200	Weak transcription	Esophagus	oesophagus
45	chr10:93608200-93624400	Strong transcription	Primary T cells from cord blood	blood
46	chr10:93608200-93625800	Strong transcription	HSMM	muscle
47	chr10:93608800-93627400	Weak transcription	Pancreas	Pancrea
48	chr10:93608800-93627600	Weak transcription	Gastric	stomach
49	chr10:93608800-93639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:93608800-93643400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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